Starting phenix.real_space_refine
on Sat Apr  6 11:44:38 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdv_17622/04_2024/8pdv_17622_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdv_17622/04_2024/8pdv_17622.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdv_17622/04_2024/8pdv_17622_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdv_17622/04_2024/8pdv_17622_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdv_17622/04_2024/8pdv_17622_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdv_17622/04_2024/8pdv_17622.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdv_17622/04_2024/8pdv_17622.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdv_17622/04_2024/8pdv_17622_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdv_17622/04_2024/8pdv_17622_updated.pdb"
  }
  resolution = 3.26
  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=   0.022
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      43      5.16       5
     C    5317      2.51       5
     N    1352      2.21       5
     O    1427      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP  155": "OD1" <-> "OD2"
    Residue "A GLU  197": "OE1" <-> "OE2"
    Residue "A ASP  316": "OD1" <-> "OD2"
    Residue "A ASP  577": "OD1" <-> "OD2"
    Residue "A GLU  590": "OE1" <-> "OE2"
    Residue "A PHE  625": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  630": "OD1" <-> "OD2"
    Residue "A PHE  699": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  767": "OD1" <-> "OD2"
    Residue "A ASP  983": "OD1" <-> "OD2"
    Residue "A PHE  999": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1044": "OE1" <-> "OE2"
    Residue "A ARG 1053": "NH1" <-> "NH2"
    Residue "A ARG 1097": "NH1" <-> "NH2"
    Residue "A ASP 1144": "OD1" <-> "OD2"
    Residue "A PHE 1176": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1183": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 8140
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1027, 8117
          Classifications: {'peptide': 1027}
          Link IDs: {'PTRANS': 30, 'TRANS': 996}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'PCG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.47, per 1000 atoms: 0.55
  Number of scatterers: 8140
  At special positions: 0
  Unit cell: (84.826, 118.552, 123.662, 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      43     16.00
     P       1     15.00
     O    1427      8.00
     N    1352      7.00
     C    5317      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: 3.19
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1938

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      42 helices and 4 sheets defined
      70.3% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 96
      removed outlier: 3.689A  pdb=" N   LEU A  94 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   PHE A  95 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 119
      removed outlier: 3.675A  pdb=" N   ASN A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 131
      removed outlier: 5.097A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 152
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 156 through 170
      removed outlier: 5.059A  pdb=" N   SER A 164 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   GLN A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 187
    Processing helix  chain 'A' and resid 195 through 206
    Processing helix  chain 'A' and resid 210 through 220
      removed outlier: 3.819A  pdb=" N   VAL A 214 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 253
      removed outlier: 3.618A  pdb=" N   LYS A 250 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   MET A 251 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 292
      removed outlier: 4.041A  pdb=" N   VAL A 265 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 266 " --> pdb=" O   GLY A 262 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   GLY A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      Proline residue:  A 276  - end of helix
      removed outlier: 3.581A  pdb=" N   HIS A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 317
      removed outlier: 3.582A  pdb=" N   TYR A 312 " --> pdb=" O   THR A 308 " (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
      removed outlier: 3.553A  pdb=" N   PHE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
    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 405
      removed outlier: 3.766A  pdb=" N   PHE A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 412
      removed outlier: 3.538A  pdb=" N   ARG A 412 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 427
    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: 4.936A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 513
    Processing helix  chain 'A' and resid 523 through 529
    Processing helix  chain 'A' and resid 572 through 599
      removed outlier: 4.268A  pdb=" N   ASP A 577 " --> pdb=" O   ARG A 573 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   MET A 578 " --> pdb=" O   GLU A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 620
    Processing helix  chain 'A' and resid 628 through 633
      removed outlier: 4.828A  pdb=" N   LYS A 633 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 652
      removed outlier: 3.735A  pdb=" N   ILE A 652 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 656
      No H-bonds generated for 'chain 'A' and resid 654 through 656'
    Processing helix  chain 'A' and resid 670 through 676
    Processing helix  chain 'A' and resid 678 through 705
      removed outlier: 4.410A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
      removed outlier: 3.707A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 760
      removed outlier: 7.599A  pdb=" N   ARG A 756 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   HIS A 757 " --> pdb=" O   GLY A 753 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   TYR A 758 " --> pdb=" O   LEU A 754 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   ILE A 759 " --> pdb=" O   GLY A 755 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   VAL A 760 " --> pdb=" O   ARG A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 762 through 777
      removed outlier: 3.841A  pdb=" N   LEU A 771 " --> pdb=" O   ASP A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 799 through 857
      removed outlier: 3.664A  pdb=" N   PHE A 802 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ARG A 803 " --> pdb=" O   LYS A 800 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLY A 807 " --> pdb=" O   LEU A 804 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   LEU A 808 " --> pdb=" O   LEU A 805 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU A 813 " --> pdb=" O   MET A 810 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   LYS A 815 " --> pdb=" O   ARG A 812 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ILE A 818 " --> pdb=" O   LYS A 815 " (cutoff:3.500A)
      Proline residue:  A 819  - end of helix
      removed outlier: 3.588A  pdb=" N   LEU A 833 " --> pdb=" O   ASN A 830 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLY A 851 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ILE A 854 " --> pdb=" O   GLY A 851 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ASP A 855 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 888
      removed outlier: 3.603A  pdb=" N   LEU A 885 " --> pdb=" O   GLU A 881 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLN A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG A 887 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 918
      removed outlier: 3.555A  pdb=" N   ILE A 913 " --> pdb=" O   SER A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 924 through 943
      removed outlier: 3.721A  pdb=" N   THR A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   MET A 942 " --> pdb=" O   MET A 938 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ASN A 943 " --> pdb=" O   LYS A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 959
      removed outlier: 3.649A  pdb=" N   LYS A 958 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 974
    Processing helix  chain 'A' and resid 1044 through 1047
      No H-bonds generated for 'chain 'A' and resid 1044 through 1047'
    Processing helix  chain 'A' and resid 1070 through 1079
    Processing helix  chain 'A' and resid 1086 through 1107
      removed outlier: 3.548A  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
    Processing sheet with id=  A, first strand: chain 'A' and resid 978 through 982
      removed outlier: 6.450A  pdb=" N   TYR A1066 " --> pdb=" O   ILE A1001 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   ILE A1001 " --> pdb=" O   TYR A1066 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ILE A1068 " --> pdb=" O   PHE A 999 " (cutoff:3.500A)
      removed outlier: 5.554A  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: 7.058A  pdb=" N   VAL A1189 " --> pdb=" O   GLU A1143 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   VAL A1145 " --> pdb=" O   PHE A1187 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   PHE A1187 " --> pdb=" O   VAL A1145 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1326 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: 2.44

  Time building geometry restraints manager: 3.37 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1770
        1.33 -     1.45: 1665
        1.45 -     1.57: 4784
        1.57 -     1.69: 2
        1.69 -     1.81: 79
  Bond restraints: 8300
  Sorted by residual:
  bond pdb=" C3' PCG A1401 "
       pdb=" C4' PCG A1401 "
    ideal  model  delta    sigma   weight residual
    1.808  1.500  0.308 2.00e-02 2.50e+03 2.37e+02
  bond pdb=" C2' PCG A1401 "
       pdb=" C3' PCG A1401 "
    ideal  model  delta    sigma   weight residual
    1.200  1.502 -0.302 2.00e-02 2.50e+03 2.27e+02
  bond pdb=" C1' PCG A1401 "
       pdb=" N9  PCG A1401 "
    ideal  model  delta    sigma   weight residual
    1.216  1.432 -0.216 2.00e-02 2.50e+03 1.17e+02
  bond pdb=" O1A PCG A1401 "
       pdb=" PA  PCG A1401 "
    ideal  model  delta    sigma   weight residual
    1.681  1.468  0.213 2.00e-02 2.50e+03 1.13e+02
  bond pdb=" C5  PCG A1401 "
       pdb=" C6  PCG A1401 "
    ideal  model  delta    sigma   weight residual
    1.532  1.322  0.210 2.00e-02 2.50e+03 1.11e+02
  ... (remaining 8295 not shown)

  Histogram of bond angle deviations from ideal:
       99.65 -   106.51: 197
      106.51 -   113.37: 4768
      113.37 -   120.23: 3050
      120.23 -   127.09: 3153
      127.09 -   133.95: 90
  Bond angle restraints: 11258
  Sorted by residual:
  angle pdb=" N   VAL A1047 "
        pdb=" CA  VAL A1047 "
        pdb=" C   VAL A1047 "
      ideal   model   delta    sigma   weight residual
     111.45  107.63    3.82 9.30e-01 1.16e+00 1.69e+01
  angle pdb=" CA  LEU A 998 "
        pdb=" C   LEU A 998 "
        pdb=" O   LEU A 998 "
      ideal   model   delta    sigma   weight residual
     121.99  117.73    4.26 1.14e+00 7.69e-01 1.40e+01
  angle pdb=" N   MET A1045 "
        pdb=" CA  MET A1045 "
        pdb=" C   MET A1045 "
      ideal   model   delta    sigma   weight residual
     113.02  108.57    4.45 1.20e+00 6.94e-01 1.38e+01
  angle pdb=" O1A PCG A1401 "
        pdb=" PA  PCG A1401 "
        pdb=" O2A PCG A1401 "
      ideal   model   delta    sigma   weight residual
     109.32  119.41  -10.09 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" CB  MET A 925 "
        pdb=" CG  MET A 925 "
        pdb=" SD  MET A 925 "
      ideal   model   delta    sigma   weight residual
     112.70  122.38   -9.68 3.00e+00 1.11e-01 1.04e+01
  ... (remaining 11253 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.20: 4682
       22.20 -    44.41: 240
       44.41 -    66.61: 26
       66.61 -    88.81: 6
       88.81 -   111.02: 2
  Dihedral angle restraints: 4956
    sinusoidal: 1968
      harmonic: 2988
  Sorted by residual:
  dihedral pdb=" C5' PCG A1401 "
           pdb=" O5' PCG A1401 "
           pdb=" PA  PCG A1401 "
           pdb=" O3' PCG A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -50.69   60.33 -111.02     1      3.00e+01 1.11e-03 1.45e+01
  dihedral pdb=" C4' PCG A1401 "
           pdb=" C5' PCG A1401 "
           pdb=" O5' PCG A1401 "
           pdb=" PA  PCG A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.20  -46.12   99.32     1      3.00e+01 1.11e-03 1.24e+01
  dihedral pdb=" CA  GLN A1106 "
           pdb=" C   GLN A1106 "
           pdb=" N   MET A1107 "
           pdb=" CA  MET A1107 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.59  -15.41     0      5.00e+00 4.00e-02 9.49e+00
  ... (remaining 4953 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 1339
       0.117 -    0.235: 14
       0.235 -    0.352: 0
       0.352 -    0.469: 0
       0.469 -    0.587: 1
  Chirality restraints: 1354
  Sorted by residual:
  chirality pdb=" C3' PCG A1401 "
            pdb=" C2' PCG A1401 "
            pdb=" C4' PCG A1401 "
            pdb=" O3' PCG A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.10   -2.69    0.59 2.00e-01 2.50e+01 8.60e+00
  chirality pdb=" C2' PCG A1401 "
            pdb=" C1' PCG A1401 "
            pdb=" C3' PCG A1401 "
            pdb=" O2' PCG A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.64    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ILE A1042 "
            pdb=" N   ILE A1042 "
            pdb=" C   ILE A1042 "
            pdb=" CB  ILE A1042 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 1351 not shown)

  Planarity restraints: 1379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1097 "   -0.191 9.50e-02 1.11e+02   8.56e-02 4.50e+00
        pdb=" NE  ARG A1097 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1097 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1097 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1097 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1096 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   ILE A1096 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ILE A1096 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A1097 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1045 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.64e+00
        pdb=" C   MET A1045 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   MET A1045 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLY A1046 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1376 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1709
        2.78 -     3.31: 8464
        3.31 -     3.84: 12773
        3.84 -     4.37: 15157
        4.37 -     4.90: 25648
  Nonbonded interactions: 63751
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A1144 "
            pdb=" N   VAL A1145 "
     model   vdw
     2.247 2.520
  nonbonded pdb=" OD1 ASP A 923 "
            pdb=" N   GLU A 924 "
     model   vdw
     2.308 2.520
  nonbonded pdb=" OH  TYR A 392 "
            pdb=" OD1 ASN A 470 "
     model   vdw
     2.361 2.440
  nonbonded pdb=" O   ASN A1154 "
            pdb=" N   ARG A1158 "
     model   vdw
     2.381 2.520
  nonbonded pdb=" O   VAL A 468 "
            pdb=" OG1 THR A 472 "
     model   vdw
     2.391 2.440
  ... (remaining 63746 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.290
  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:          5.850
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     24.740
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
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      :  0.009   0.308   8300  Z= 0.625
  Angle     :  0.571  10.094  11258  Z= 0.322
  Chirality :  0.042   0.587   1354
  Planarity :  0.004   0.086   1379
  Dihedral  : 13.391 111.018   3018
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.80 %
    Favored  : 93.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.27), residues: 1015
  helix:  1.49 (0.19), residues: 727
  sheet:  0.62 (0.72), residues: 48
  loop :  0.12 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 278 
 HIS   0.002   0.001   HIS A 676 
 PHE   0.017   0.001   PHE A 201 
 TYR   0.010   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A 733 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 264
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7905 (mttm) cc_final: 0.7689 (mttm)
REVERT: A   84 SER cc_start: 0.7750 (p) cc_final: 0.7485 (t)
REVERT: A  116 VAL cc_start: 0.6947 (p) cc_final: 0.6681 (m)
REVERT: A  120 VAL cc_start: 0.7218 (t) cc_final: 0.7001 (p)
REVERT: A  124 GLU cc_start: 0.7468 (tt0) cc_final: 0.6974 (tm-30)
REVERT: A  155 ASP cc_start: 0.7711 (t70) cc_final: 0.7258 (t0)
REVERT: A  175 VAL cc_start: 0.7056 (t) cc_final: 0.6828 (m)
REVERT: A  187 ASN cc_start: 0.7318 (m-40) cc_final: 0.6808 (m-40)
REVERT: A  263 GLN cc_start: 0.6218 (mm-40) cc_final: 0.5954 (mm-40)
REVERT: A  289 PHE cc_start: 0.8187 (m-80) cc_final: 0.7983 (m-80)
REVERT: A  295 ASN cc_start: 0.8260 (t0) cc_final: 0.7937 (t0)
REVERT: A  344 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7454 (mm-30)
REVERT: A  354 GLU cc_start: 0.7928 (tt0) cc_final: 0.7699 (mt-10)
REVERT: A  355 MET cc_start: 0.7773 (tmm) cc_final: 0.7509 (tmm)
REVERT: A  383 MET cc_start: 0.7899 (mmm) cc_final: 0.7540 (mmm)
REVERT: A  474 ILE cc_start: 0.7717 (tp) cc_final: 0.7420 (tt)
REVERT: A  485 ASP cc_start: 0.7604 (m-30) cc_final: 0.7344 (m-30)
REVERT: A  511 MET cc_start: 0.7457 (tmm) cc_final: 0.7019 (tmm)
REVERT: A  531 GLU cc_start: 0.7532 (tt0) cc_final: 0.7214 (tp30)
REVERT: A  579 MET cc_start: 0.6495 (tpt) cc_final: 0.6271 (tpt)
REVERT: A  585 ARG cc_start: 0.6990 (mtt-85) cc_final: 0.6460 (mtt-85)
REVERT: A  588 LYS cc_start: 0.7849 (ttpp) cc_final: 0.7512 (ttpp)
REVERT: A  628 VAL cc_start: 0.7706 (m) cc_final: 0.7354 (t)
REVERT: A  634 SER cc_start: 0.8034 (m) cc_final: 0.7706 (p)
REVERT: A  646 ARG cc_start: 0.7598 (ttp-170) cc_final: 0.7357 (ttp-170)
REVERT: A  647 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7424 (mptt)
REVERT: A  684 ILE cc_start: 0.7197 (mm) cc_final: 0.6752 (pt)
REVERT: A  697 MET cc_start: 0.5542 (tpp) cc_final: 0.5107 (tpp)
REVERT: A  815 LYS cc_start: 0.8364 (tttm) cc_final: 0.8092 (tttp)
REVERT: A  828 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8204 (mmmt)
REVERT: A  838 ASP cc_start: 0.7577 (m-30) cc_final: 0.7228 (m-30)
REVERT: A  841 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7410 (tptt)
REVERT: A  845 ILE cc_start: 0.8044 (mt) cc_final: 0.7810 (mm)
REVERT: A  862 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7556 (tppt)
REVERT: A  865 ARG cc_start: 0.6725 (tmm-80) cc_final: 0.6519 (tmm-80)
REVERT: A  866 GLU cc_start: 0.7360 (tp30) cc_final: 0.6711 (tp30)
REVERT: A  867 LEU cc_start: 0.7761 (mp) cc_final: 0.7441 (mm)
REVERT: A  868 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7373 (mtmm)
REVERT: A  870 ILE cc_start: 0.8005 (mt) cc_final: 0.7634 (mt)
REVERT: A  877 GLN cc_start: 0.7815 (mt0) cc_final: 0.7540 (tt0)
REVERT: A  888 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7252 (mm-30)
REVERT: A  911 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7244 (mm-30)
REVERT: A  931 GLU cc_start: 0.7583 (tt0) cc_final: 0.7356 (tt0)
REVERT: A  946 SER cc_start: 0.8169 (p) cc_final: 0.7956 (t)
REVERT: A  961 SER cc_start: 0.8303 (m) cc_final: 0.7975 (p)
REVERT: A  972 PHE cc_start: 0.7915 (t80) cc_final: 0.7625 (t80)
REVERT: A  974 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7566 (mtpp)
REVERT: A  999 PHE cc_start: 0.7627 (m-80) cc_final: 0.7298 (m-80)
REVERT: A 1003 SER cc_start: 0.8647 (t) cc_final: 0.8266 (t)
REVERT: A 1033 GLU cc_start: 0.7258 (tt0) cc_final: 0.6978 (tt0)
REVERT: A 1096 ILE cc_start: 0.7975 (mt) cc_final: 0.7677 (mm)
REVERT: A 1107 MET cc_start: 0.6480 (mtm) cc_final: 0.6141 (mtp)
REVERT: A 1118 LYS cc_start: 0.3998 (tmtt) cc_final: 0.2876 (mttm)
REVERT: A 1122 GLU cc_start: 0.7677 (tp30) cc_final: 0.7370 (tt0)
REVERT: A 1133 HIS cc_start: 0.6864 (t-170) cc_final: 0.6622 (t-90)
REVERT: A 1143 GLU cc_start: 0.7176 (tt0) cc_final: 0.6759 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7138 (t0) cc_final: 0.6626 (t0)
REVERT: A 1182 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6179 (mp0)
REVERT: A 1186 LEU cc_start: 0.8455 (tp) cc_final: 0.8189 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 265
  average time/residue: 0.2397
  time to fit residues: 82.3200
Evaluate side-chains
  224 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 77 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0870
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.3980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.4336

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8300  Z= 0.187
  Angle     :  0.527   7.958  11258  Z= 0.280
  Chirality :  0.040   0.182   1354
  Planarity :  0.005   0.048   1379
  Dihedral  :  5.149  85.402   1105
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 10.87 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.26), residues: 1015
  helix:  1.47 (0.19), residues: 722
  sheet:  1.24 (0.74), residues: 46
  loop :  0.30 (0.43), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 278 
 HIS   0.003   0.001   HIS A 676 
 PHE   0.011   0.001   PHE A 352 
 TYR   0.015   0.001   TYR A 743 
 ARG   0.003   0.000   ARG A1169 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 227
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7683 (mttm) cc_final: 0.7442 (mttm)
REVERT: A   84 SER cc_start: 0.7312 (p) cc_final: 0.7086 (t)
REVERT: A  120 VAL cc_start: 0.7027 (t) cc_final: 0.6676 (p)
REVERT: A  124 GLU cc_start: 0.7437 (tt0) cc_final: 0.7020 (tm-30)
REVERT: A  155 ASP cc_start: 0.8046 (t70) cc_final: 0.7570 (t0)
REVERT: A  169 LEU cc_start: 0.7996 (tp) cc_final: 0.7734 (tp)
REVERT: A  187 ASN cc_start: 0.7220 (m-40) cc_final: 0.6747 (m-40)
REVERT: A  205 MET cc_start: 0.7918 (tpp) cc_final: 0.7688 (mmt)
REVERT: A  344 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7309 (mm-30)
REVERT: A  354 GLU cc_start: 0.7915 (tt0) cc_final: 0.7454 (mt-10)
REVERT: A  355 MET cc_start: 0.7903 (tmm) cc_final: 0.7345 (tmm)
REVERT: A  375 LYS cc_start: 0.7563 (mttt) cc_final: 0.7238 (mttt)
REVERT: A  383 MET cc_start: 0.7753 (mmm) cc_final: 0.7265 (mmm)
REVERT: A  401 MET cc_start: 0.6940 (mtp) cc_final: 0.6691 (mtm)
REVERT: A  443 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7139 (tp30)
REVERT: A  474 ILE cc_start: 0.7538 (tp) cc_final: 0.7258 (tt)
REVERT: A  485 ASP cc_start: 0.7662 (m-30) cc_final: 0.7389 (m-30)
REVERT: A  486 ILE cc_start: 0.8463 (mt) cc_final: 0.8154 (mm)
REVERT: A  511 MET cc_start: 0.7585 (tmm) cc_final: 0.7142 (tmm)
REVERT: A  531 GLU cc_start: 0.7529 (tt0) cc_final: 0.7222 (tp30)
REVERT: A  588 LYS cc_start: 0.7652 (ttpp) cc_final: 0.7326 (ttpp)
REVERT: A  628 VAL cc_start: 0.7592 (m) cc_final: 0.7276 (t)
REVERT: A  629 ASP cc_start: 0.7905 (p0) cc_final: 0.7609 (p0)
REVERT: A  633 LYS cc_start: 0.8373 (mttt) cc_final: 0.7930 (mmtm)
REVERT: A  634 SER cc_start: 0.8094 (m) cc_final: 0.7738 (p)
REVERT: A  646 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7297 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7122 (mm) cc_final: 0.6683 (pt)
REVERT: A  697 MET cc_start: 0.5513 (tpp) cc_final: 0.5001 (tpp)
REVERT: A  815 LYS cc_start: 0.8380 (tttm) cc_final: 0.8110 (tttp)
REVERT: A  828 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7892 (mmtm)
REVERT: A  838 ASP cc_start: 0.7386 (m-30) cc_final: 0.7144 (m-30)
REVERT: A  841 LYS cc_start: 0.7573 (ttpp) cc_final: 0.7272 (tptt)
REVERT: A  862 LYS cc_start: 0.7700 (ttmm) cc_final: 0.7130 (ttmt)
REVERT: A  865 ARG cc_start: 0.6639 (tmm-80) cc_final: 0.6411 (tmm-80)
REVERT: A  866 GLU cc_start: 0.7071 (tp30) cc_final: 0.6686 (tp30)
REVERT: A  876 LEU cc_start: 0.8051 (mt) cc_final: 0.7741 (mm)
REVERT: A  877 GLN cc_start: 0.7941 (mt0) cc_final: 0.7608 (tt0)
REVERT: A  900 GLN cc_start: 0.7996 (mm110) cc_final: 0.7698 (mm-40)
REVERT: A  931 GLU cc_start: 0.7483 (tt0) cc_final: 0.7211 (tt0)
REVERT: A  961 SER cc_start: 0.8291 (m) cc_final: 0.7943 (p)
REVERT: A  974 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7665 (mtpp)
REVERT: A  999 PHE cc_start: 0.7713 (m-80) cc_final: 0.7403 (m-80)
REVERT: A 1003 SER cc_start: 0.8158 (t) cc_final: 0.7774 (t)
REVERT: A 1033 GLU cc_start: 0.7354 (tt0) cc_final: 0.7064 (tt0)
REVERT: A 1096 ILE cc_start: 0.7969 (mt) cc_final: 0.7704 (mm)
REVERT: A 1118 LYS cc_start: 0.4147 (tmtt) cc_final: 0.2491 (tppt)
REVERT: A 1122 GLU cc_start: 0.7538 (tp30) cc_final: 0.7069 (tt0)
REVERT: A 1123 ARG cc_start: 0.7196 (mmt180) cc_final: 0.6855 (mmt-90)
REVERT: A 1133 HIS cc_start: 0.6779 (t-170) cc_final: 0.6560 (t-90)
REVERT: A 1143 GLU cc_start: 0.7177 (tt0) cc_final: 0.6716 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7305 (t0) cc_final: 0.6807 (t0)
REVERT: A 1182 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6188 (mp0)
REVERT: A 1186 LEU cc_start: 0.8469 (tp) cc_final: 0.8226 (tp)
  outliers start: 22
  outliers final: 12
  residues processed: 236
  average time/residue: 0.2221
  time to fit residues: 68.9731
Evaluate side-chains
  227 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 215
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  983 ASP
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1061 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 28 optimal weight:    0.3980
   chunk 77 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 350 HIS
A 886 GLN
A 908 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8300  Z= 0.232
  Angle     :  0.501   8.220  11258  Z= 0.264
  Chirality :  0.040   0.201   1354
  Planarity :  0.005   0.050   1379
  Dihedral  :  4.963  81.072   1105
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.04 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.26), residues: 1015
  helix:  1.24 (0.19), residues: 723
  sheet:  1.20 (0.72), residues: 51
  loop :  0.13 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.014   0.001   PHE A 575 
 TYR   0.013   0.001   TYR A 309 
 ARG   0.003   0.000   ARG A1169 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7733 (mttm) cc_final: 0.7509 (mttm)
REVERT: A  120 VAL cc_start: 0.6992 (t) cc_final: 0.6647 (p)
REVERT: A  124 GLU cc_start: 0.7630 (tt0) cc_final: 0.6992 (tm-30)
REVERT: A  155 ASP cc_start: 0.7957 (t70) cc_final: 0.7222 (t0)
REVERT: A  187 ASN cc_start: 0.7259 (m-40) cc_final: 0.6810 (m-40)
REVERT: A  296 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7512 (t0)
REVERT: A  344 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7312 (mm-30)
REVERT: A  355 MET cc_start: 0.7937 (tmm) cc_final: 0.7349 (tmm)
REVERT: A  375 LYS cc_start: 0.7729 (mttt) cc_final: 0.7394 (mttt)
REVERT: A  383 MET cc_start: 0.7828 (mmm) cc_final: 0.7447 (mmm)
REVERT: A  443 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7158 (tp30)
REVERT: A  474 ILE cc_start: 0.7579 (tp) cc_final: 0.7279 (tt)
REVERT: A  485 ASP cc_start: 0.7665 (m-30) cc_final: 0.7387 (m-30)
REVERT: A  486 ILE cc_start: 0.8485 (mt) cc_final: 0.8148 (mm)
REVERT: A  511 MET cc_start: 0.7623 (tmm) cc_final: 0.7169 (tmm)
REVERT: A  588 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7364 (ttpp)
REVERT: A  596 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7807 (ttmt)
REVERT: A  628 VAL cc_start: 0.7695 (m) cc_final: 0.7417 (t)
REVERT: A  633 LYS cc_start: 0.8418 (mttt) cc_final: 0.7955 (mmtm)
REVERT: A  634 SER cc_start: 0.8089 (m) cc_final: 0.7734 (p)
REVERT: A  646 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.7315 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7141 (mm) cc_final: 0.6684 (pt)
REVERT: A  697 MET cc_start: 0.5529 (tpp) cc_final: 0.5059 (tpp)
REVERT: A  815 LYS cc_start: 0.8390 (tttm) cc_final: 0.8117 (tttp)
REVERT: A  828 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7754 (mmtm)
REVERT: A  841 LYS cc_start: 0.7577 (ttpp) cc_final: 0.7283 (tptt)
REVERT: A  862 LYS cc_start: 0.7716 (ttmm) cc_final: 0.6965 (ttmt)
REVERT: A  865 ARG cc_start: 0.6689 (tmm-80) cc_final: 0.6447 (tmm-80)
REVERT: A  866 GLU cc_start: 0.6959 (tp30) cc_final: 0.6483 (tp30)
REVERT: A  877 GLN cc_start: 0.7959 (mt0) cc_final: 0.7654 (tt0)
REVERT: A  900 GLN cc_start: 0.8011 (mm110) cc_final: 0.7684 (mm-40)
REVERT: A  961 SER cc_start: 0.8362 (m) cc_final: 0.8027 (p)
REVERT: A  974 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7646 (mtpp)
REVERT: A  994 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6171 (tp30)
REVERT: A  999 PHE cc_start: 0.7698 (m-80) cc_final: 0.7393 (m-80)
REVERT: A 1003 SER cc_start: 0.8117 (t) cc_final: 0.7729 (t)
REVERT: A 1033 GLU cc_start: 0.7439 (tt0) cc_final: 0.7172 (tt0)
REVERT: A 1110 GLN cc_start: 0.7734 (mp10) cc_final: 0.7019 (mp10)
REVERT: A 1118 LYS cc_start: 0.4396 (tmtt) cc_final: 0.2470 (tppt)
REVERT: A 1122 GLU cc_start: 0.7574 (tp30) cc_final: 0.7255 (tp30)
REVERT: A 1143 GLU cc_start: 0.7207 (tt0) cc_final: 0.6740 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7384 (t0) cc_final: 0.6869 (t0)
REVERT: A 1182 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6198 (mp0)
REVERT: A 1186 LEU cc_start: 0.8552 (tp) cc_final: 0.8121 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 233
  average time/residue: 0.2270
  time to fit residues: 70.0493
Evaluate side-chains
  231 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 214
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  983 ASP
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1061 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 93 optimal weight:    0.5980
   chunk 98 optimal weight:    0.0770
   chunk 88 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 600 HIS
A 914 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8300  Z= 0.193
  Angle     :  0.480   6.604  11258  Z= 0.253
  Chirality :  0.039   0.207   1354
  Planarity :  0.004   0.045   1379
  Dihedral  :  4.670  72.288   1105
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.29 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.26), residues: 1015
  helix:  1.29 (0.19), residues: 720
  sheet:  1.38 (0.73), residues: 51
  loop : -0.02 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A1172 
 PHE   0.011   0.001   PHE A1136 
 TYR   0.010   0.001   TYR A1066 
 ARG   0.003   0.000   ARG A 976 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 213
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.7444 (mm) cc_final: 0.7206 (mt)
REVERT: A  120 VAL cc_start: 0.7019 (t) cc_final: 0.6454 (p)
REVERT: A  124 GLU cc_start: 0.7578 (tt0) cc_final: 0.6967 (mt-10)
REVERT: A  155 ASP cc_start: 0.7969 (t70) cc_final: 0.7219 (t0)
REVERT: A  161 ARG cc_start: 0.7356 (mtm180) cc_final: 0.7096 (mtt180)
REVERT: A  187 ASN cc_start: 0.7208 (m-40) cc_final: 0.6795 (m-40)
REVERT: A  233 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7504 (tt0)
REVERT: A  296 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7414 (t0)
REVERT: A  344 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7284 (mm-30)
REVERT: A  355 MET cc_start: 0.7939 (tmm) cc_final: 0.7322 (tmm)
REVERT: A  375 LYS cc_start: 0.7771 (mttt) cc_final: 0.7458 (mttt)
REVERT: A  383 MET cc_start: 0.7800 (mmm) cc_final: 0.7451 (mmm)
REVERT: A  443 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7133 (tp30)
REVERT: A  474 ILE cc_start: 0.7538 (tp) cc_final: 0.7241 (tt)
REVERT: A  485 ASP cc_start: 0.7660 (m-30) cc_final: 0.7384 (m-30)
REVERT: A  486 ILE cc_start: 0.8489 (mt) cc_final: 0.8118 (mm)
REVERT: A  511 MET cc_start: 0.7645 (tmm) cc_final: 0.7183 (tmm)
REVERT: A  584 LEU cc_start: 0.7783 (mt) cc_final: 0.7582 (mm)
REVERT: A  588 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7351 (ttpp)
REVERT: A  628 VAL cc_start: 0.7648 (m) cc_final: 0.7393 (t)
REVERT: A  633 LYS cc_start: 0.8406 (mttt) cc_final: 0.7950 (mmtm)
REVERT: A  634 SER cc_start: 0.8091 (m) cc_final: 0.7727 (p)
REVERT: A  646 ARG cc_start: 0.7628 (ttp-170) cc_final: 0.7298 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7133 (mm) cc_final: 0.6672 (pt)
REVERT: A  697 MET cc_start: 0.5542 (tpp) cc_final: 0.5051 (tpp)
REVERT: A  815 LYS cc_start: 0.8395 (tttm) cc_final: 0.8125 (tttp)
REVERT: A  828 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7663 (mmmt)
REVERT: A  841 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7266 (mmtt)
REVERT: A  852 LYS cc_start: 0.8304 (mmtm) cc_final: 0.7774 (mmmm)
REVERT: A  866 GLU cc_start: 0.6856 (tp30) cc_final: 0.6347 (tp30)
REVERT: A  877 GLN cc_start: 0.7964 (mt0) cc_final: 0.7639 (tt0)
REVERT: A  900 GLN cc_start: 0.7985 (mm110) cc_final: 0.7592 (mm-40)
REVERT: A  961 SER cc_start: 0.8355 (m) cc_final: 0.8029 (p)
REVERT: A  974 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7642 (mtpp)
REVERT: A  994 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6177 (tp30)
REVERT: A  999 PHE cc_start: 0.7788 (m-80) cc_final: 0.7484 (m-80)
REVERT: A 1003 SER cc_start: 0.8170 (t) cc_final: 0.7763 (t)
REVERT: A 1033 GLU cc_start: 0.7445 (tt0) cc_final: 0.7183 (tt0)
REVERT: A 1110 GLN cc_start: 0.7763 (mp10) cc_final: 0.7111 (mp10)
REVERT: A 1118 LYS cc_start: 0.3856 (tmtt) cc_final: 0.2098 (tppt)
REVERT: A 1122 GLU cc_start: 0.7610 (tp30) cc_final: 0.7370 (tp30)
REVERT: A 1143 GLU cc_start: 0.7207 (tt0) cc_final: 0.6754 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7358 (t0) cc_final: 0.6911 (t0)
REVERT: A 1186 LEU cc_start: 0.8509 (tp) cc_final: 0.8105 (tp)
  outliers start: 28
  outliers final: 20
  residues processed: 229
  average time/residue: 0.2304
  time to fit residues: 69.4370
Evaluate side-chains
  233 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  924 GLU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1100 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 33 optimal weight:    0.0030
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
A 691 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8300  Z= 0.175
  Angle     :  0.463   6.476  11258  Z= 0.242
  Chirality :  0.039   0.209   1354
  Planarity :  0.004   0.055   1379
  Dihedral  :  4.294  57.309   1105
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.65 %
    Favored  : 80.07 %
  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:  1.50 (0.26), residues: 1015
  helix:  1.39 (0.19), residues: 717
  sheet:  1.49 (0.74), residues: 51
  loop : -0.09 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 278 
 HIS   0.003   0.001   HIS A 676 
 PHE   0.012   0.001   PHE A1136 
 TYR   0.009   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A1169 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 213
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 VAL cc_start: 0.6996 (t) cc_final: 0.6515 (p)
REVERT: A  124 GLU cc_start: 0.7490 (tt0) cc_final: 0.6935 (mt-10)
REVERT: A  140 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7675 (mp10)
REVERT: A  155 ASP cc_start: 0.7958 (t70) cc_final: 0.7217 (t0)
REVERT: A  161 ARG cc_start: 0.7350 (mtm180) cc_final: 0.7100 (mtt180)
REVERT: A  187 ASN cc_start: 0.7223 (m-40) cc_final: 0.6858 (m-40)
REVERT: A  220 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6312 (mp)
REVERT: A  320 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7732 (mp0)
REVERT: A  344 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7264 (mm-30)
REVERT: A  355 MET cc_start: 0.7934 (tmm) cc_final: 0.7361 (tmm)
REVERT: A  366 MET cc_start: 0.8039 (mtp) cc_final: 0.7643 (mtp)
REVERT: A  375 LYS cc_start: 0.7785 (mttt) cc_final: 0.7482 (mttt)
REVERT: A  383 MET cc_start: 0.7790 (mmm) cc_final: 0.7491 (mmm)
REVERT: A  443 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7213 (tp30)
REVERT: A  485 ASP cc_start: 0.7666 (m-30) cc_final: 0.7367 (m-30)
REVERT: A  486 ILE cc_start: 0.8493 (mt) cc_final: 0.8111 (mm)
REVERT: A  511 MET cc_start: 0.7694 (tmm) cc_final: 0.7220 (tmm)
REVERT: A  588 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7355 (ttpp)
REVERT: A  628 VAL cc_start: 0.7667 (m) cc_final: 0.7426 (t)
REVERT: A  633 LYS cc_start: 0.8390 (mttt) cc_final: 0.7945 (mmtm)
REVERT: A  634 SER cc_start: 0.8100 (m) cc_final: 0.7718 (p)
REVERT: A  646 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.7263 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7170 (mm) cc_final: 0.6685 (pt)
REVERT: A  697 MET cc_start: 0.5557 (tpp) cc_final: 0.5034 (tpp)
REVERT: A  815 LYS cc_start: 0.8405 (tttm) cc_final: 0.8197 (tttp)
REVERT: A  828 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7566 (mmmt)
REVERT: A  841 LYS cc_start: 0.7572 (ttpp) cc_final: 0.7248 (mmtt)
REVERT: A  857 MET cc_start: 0.7772 (ttp) cc_final: 0.7386 (ptp)
REVERT: A  877 GLN cc_start: 0.7983 (mt0) cc_final: 0.7635 (tt0)
REVERT: A  900 GLN cc_start: 0.7975 (mm110) cc_final: 0.7676 (mm-40)
REVERT: A  961 SER cc_start: 0.8358 (m) cc_final: 0.8040 (p)
REVERT: A  974 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7605 (mtpp)
REVERT: A  999 PHE cc_start: 0.7823 (m-80) cc_final: 0.7536 (m-80)
REVERT: A 1003 SER cc_start: 0.8174 (t) cc_final: 0.7784 (t)
REVERT: A 1033 GLU cc_start: 0.7440 (tt0) cc_final: 0.7131 (tt0)
REVERT: A 1110 GLN cc_start: 0.7737 (mp10) cc_final: 0.7059 (mp10)
REVERT: A 1118 LYS cc_start: 0.3499 (tmtt) cc_final: 0.2099 (tppt)
REVERT: A 1122 GLU cc_start: 0.7596 (tp30) cc_final: 0.7324 (mt-10)
REVERT: A 1123 ARG cc_start: 0.7297 (mmt180) cc_final: 0.6337 (mmp-170)
REVERT: A 1143 GLU cc_start: 0.7225 (tt0) cc_final: 0.6766 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7346 (t0) cc_final: 0.7095 (t0)
REVERT: A 1173 LYS cc_start: 0.7472 (tppt) cc_final: 0.7136 (tppt)
REVERT: A 1186 LEU cc_start: 0.8509 (tp) cc_final: 0.8113 (tp)
  outliers start: 29
  outliers final: 21
  residues processed: 228
  average time/residue: 0.2499
  time to fit residues: 74.5892
Evaluate side-chains
  233 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 210
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  629 ASP
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  924 GLU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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: 0.7253
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8300  Z= 0.191
  Angle     :  0.467   6.304  11258  Z= 0.244
  Chirality :  0.039   0.218   1354
  Planarity :  0.004   0.045   1379
  Dihedral  :  4.038  38.594   1105
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.53 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.27), residues: 1015
  helix:  1.37 (0.19), residues: 717
  sheet:  1.49 (0.75), residues: 51
  loop : -0.07 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 278 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 972 
 TYR   0.011   0.001   TYR A 309 
 ARG   0.003   0.000   ARG A1169 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 213
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.7456 (mm) cc_final: 0.7215 (mt)
REVERT: A  120 VAL cc_start: 0.6961 (t) cc_final: 0.6555 (p)
REVERT: A  124 GLU cc_start: 0.7490 (tt0) cc_final: 0.6973 (tm-30)
REVERT: A  155 ASP cc_start: 0.7971 (t70) cc_final: 0.7167 (t0)
REVERT: A  161 ARG cc_start: 0.7337 (mtm180) cc_final: 0.7114 (mtt180)
REVERT: A  187 ASN cc_start: 0.7217 (m-40) cc_final: 0.6861 (m-40)
REVERT: A  320 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7740 (mp0)
REVERT: A  344 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7248 (mm-30)
REVERT: A  355 MET cc_start: 0.7937 (tmm) cc_final: 0.7338 (tmm)
REVERT: A  366 MET cc_start: 0.8069 (mtp) cc_final: 0.7706 (mtp)
REVERT: A  383 MET cc_start: 0.7778 (mmm) cc_final: 0.7504 (mmm)
REVERT: A  443 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7178 (tp30)
REVERT: A  450 VAL cc_start: 0.7744 (m) cc_final: 0.7458 (p)
REVERT: A  485 ASP cc_start: 0.7652 (m-30) cc_final: 0.7359 (m-30)
REVERT: A  486 ILE cc_start: 0.8481 (mt) cc_final: 0.8091 (mm)
REVERT: A  511 MET cc_start: 0.7707 (tmm) cc_final: 0.7216 (tmm)
REVERT: A  588 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7384 (ttpp)
REVERT: A  628 VAL cc_start: 0.7651 (m) cc_final: 0.7416 (t)
REVERT: A  633 LYS cc_start: 0.8394 (mttt) cc_final: 0.7942 (mmtm)
REVERT: A  634 SER cc_start: 0.8108 (m) cc_final: 0.7734 (p)
REVERT: A  684 ILE cc_start: 0.7181 (mm) cc_final: 0.6697 (pt)
REVERT: A  697 MET cc_start: 0.5635 (tpp) cc_final: 0.5091 (tpp)
REVERT: A  815 LYS cc_start: 0.8410 (tttm) cc_final: 0.8205 (tttp)
REVERT: A  828 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7533 (mmmt)
REVERT: A  841 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7248 (mmtt)
REVERT: A  857 MET cc_start: 0.7767 (ttp) cc_final: 0.7366 (ptp)
REVERT: A  877 GLN cc_start: 0.7983 (mt0) cc_final: 0.7615 (tt0)
REVERT: A  931 GLU cc_start: 0.7559 (tt0) cc_final: 0.7004 (mt-10)
REVERT: A  961 SER cc_start: 0.8383 (m) cc_final: 0.8062 (p)
REVERT: A  974 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7589 (mtpp)
REVERT: A  999 PHE cc_start: 0.7857 (m-80) cc_final: 0.7563 (m-80)
REVERT: A 1003 SER cc_start: 0.8187 (t) cc_final: 0.7797 (t)
REVERT: A 1033 GLU cc_start: 0.7436 (tt0) cc_final: 0.7103 (tt0)
REVERT: A 1110 GLN cc_start: 0.7772 (mp10) cc_final: 0.7119 (mp10)
REVERT: A 1118 LYS cc_start: 0.2937 (tmtt) cc_final: 0.1534 (tppt)
REVERT: A 1122 GLU cc_start: 0.7589 (tp30) cc_final: 0.7338 (mt-10)
REVERT: A 1123 ARG cc_start: 0.7312 (mmt180) cc_final: 0.6193 (mmp-170)
REVERT: A 1143 GLU cc_start: 0.7220 (tt0) cc_final: 0.6716 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7360 (t0) cc_final: 0.6973 (t0)
REVERT: A 1173 LYS cc_start: 0.7415 (tppt) cc_final: 0.7064 (tppt)
REVERT: A 1186 LEU cc_start: 0.8503 (tp) cc_final: 0.8110 (tp)
  outliers start: 29
  outliers final: 26
  residues processed: 229
  average time/residue: 0.2319
  time to fit residues: 70.6006
Evaluate side-chains
  235 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  629 ASP
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 83 optimal weight:    0.3980
   chunk 98 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 58 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
A 900 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8300  Z= 0.256
  Angle     :  0.492   6.508  11258  Z= 0.258
  Chirality :  0.040   0.233   1354
  Planarity :  0.005   0.061   1379
  Dihedral  :  4.002  23.226   1105
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.44 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.27), residues: 1015
  helix:  1.28 (0.19), residues: 717
  sheet:  1.42 (0.75), residues: 51
  loop : -0.16 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.014   0.001   PHE A 982 
 TYR   0.013   0.001   TYR A 309 
 ARG   0.003   0.000   ARG A1169 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 218
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.7435 (mm) cc_final: 0.7190 (mt)
REVERT: A  120 VAL cc_start: 0.6947 (t) cc_final: 0.6549 (p)
REVERT: A  124 GLU cc_start: 0.7497 (tt0) cc_final: 0.7019 (tm-30)
REVERT: A  140 GLN cc_start: 0.7880 (mp-120) cc_final: 0.7544 (mp10)
REVERT: A  155 ASP cc_start: 0.7855 (t70) cc_final: 0.7071 (t0)
REVERT: A  161 ARG cc_start: 0.7336 (mtm180) cc_final: 0.7053 (mtt180)
REVERT: A  187 ASN cc_start: 0.7223 (m-40) cc_final: 0.6869 (m-40)
REVERT: A  229 ILE cc_start: 0.7935 (mm) cc_final: 0.7572 (mm)
REVERT: A  320 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7672 (mp0)
REVERT: A  344 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7260 (mm-30)
REVERT: A  355 MET cc_start: 0.7920 (tmm) cc_final: 0.7298 (tmm)
REVERT: A  366 MET cc_start: 0.8141 (mtp) cc_final: 0.7819 (mtp)
REVERT: A  383 MET cc_start: 0.7780 (mmm) cc_final: 0.7537 (mmm)
REVERT: A  443 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7184 (tp30)
REVERT: A  450 VAL cc_start: 0.7735 (m) cc_final: 0.7430 (p)
REVERT: A  485 ASP cc_start: 0.7657 (m-30) cc_final: 0.7350 (m-30)
REVERT: A  486 ILE cc_start: 0.8477 (mt) cc_final: 0.8080 (mm)
REVERT: A  511 MET cc_start: 0.7707 (tmm) cc_final: 0.7207 (tmm)
REVERT: A  588 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7394 (ttpp)
REVERT: A  628 VAL cc_start: 0.7690 (m) cc_final: 0.7426 (t)
REVERT: A  633 LYS cc_start: 0.8395 (mttt) cc_final: 0.7957 (mmtm)
REVERT: A  634 SER cc_start: 0.8107 (m) cc_final: 0.7738 (p)
REVERT: A  684 ILE cc_start: 0.7195 (mm) cc_final: 0.6714 (pt)
REVERT: A  697 MET cc_start: 0.5661 (tpp) cc_final: 0.5110 (tpp)
REVERT: A  815 LYS cc_start: 0.8429 (tttm) cc_final: 0.8223 (tttp)
REVERT: A  828 LYS cc_start: 0.7866 (mmmt) cc_final: 0.7618 (mmmt)
REVERT: A  841 LYS cc_start: 0.7578 (ttpp) cc_final: 0.7251 (mmtt)
REVERT: A  852 LYS cc_start: 0.8299 (mmtp) cc_final: 0.7878 (mmmm)
REVERT: A  857 MET cc_start: 0.7789 (ttp) cc_final: 0.7396 (ptp)
REVERT: A  877 GLN cc_start: 0.8013 (mt0) cc_final: 0.7584 (tt0)
REVERT: A  900 GLN cc_start: 0.8025 (mm110) cc_final: 0.7657 (mm-40)
REVERT: A  961 SER cc_start: 0.8424 (m) cc_final: 0.8106 (p)
REVERT: A  974 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7598 (mtpp)
REVERT: A  999 PHE cc_start: 0.7958 (m-80) cc_final: 0.7749 (m-80)
REVERT: A 1003 SER cc_start: 0.8161 (t) cc_final: 0.7780 (t)
REVERT: A 1110 GLN cc_start: 0.7805 (mp10) cc_final: 0.7120 (mp10)
REVERT: A 1118 LYS cc_start: 0.2923 (tmtt) cc_final: 0.1733 (mttm)
REVERT: A 1122 GLU cc_start: 0.7624 (tp30) cc_final: 0.7351 (mt-10)
REVERT: A 1123 ARG cc_start: 0.7346 (mmt180) cc_final: 0.6658 (mmt-90)
REVERT: A 1143 GLU cc_start: 0.7202 (tt0) cc_final: 0.6738 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7354 (t0) cc_final: 0.7004 (t0)
REVERT: A 1186 LEU cc_start: 0.8520 (tp) cc_final: 0.8118 (tp)
  outliers start: 28
  outliers final: 24
  residues processed: 232
  average time/residue: 0.2311
  time to fit residues: 70.7541
Evaluate side-chains
  236 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 211
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  629 ASP
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.0170
   chunk 62 optimal weight:    9.9990
   chunk 66 optimal weight:    0.0270
   chunk 48 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 89 optimal weight:    0.4980
   chunk 94 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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: 0.7243
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8300  Z= 0.164
  Angle     :  0.453   6.172  11258  Z= 0.240
  Chirality :  0.038   0.228   1354
  Planarity :  0.004   0.054   1379
  Dihedral  :  3.862  24.623   1105
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.12 %
    Favored  : 79.05 %
  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:  1.54 (0.27), residues: 1015
  helix:  1.40 (0.19), residues: 717
  sheet:  1.50 (0.75), residues: 51
  loop : -0.01 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.009   0.001   PHE A1136 
 TYR   0.009   0.001   TYR A1066 
 ARG   0.003   0.000   ARG A1169 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 213
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.7423 (mm) cc_final: 0.7184 (mt)
REVERT: A  120 VAL cc_start: 0.6889 (t) cc_final: 0.6493 (p)
REVERT: A  124 GLU cc_start: 0.7489 (tt0) cc_final: 0.7004 (tm-30)
REVERT: A  140 GLN cc_start: 0.7905 (mp-120) cc_final: 0.7571 (mp10)
REVERT: A  155 ASP cc_start: 0.7826 (t70) cc_final: 0.7020 (t0)
REVERT: A  187 ASN cc_start: 0.7286 (m-40) cc_final: 0.6923 (m-40)
REVERT: A  320 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7692 (mp0)
REVERT: A  344 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7254 (mm-30)
REVERT: A  355 MET cc_start: 0.7918 (tmm) cc_final: 0.7377 (tmm)
REVERT: A  366 MET cc_start: 0.8079 (mtp) cc_final: 0.7727 (mtp)
REVERT: A  383 MET cc_start: 0.7782 (mmm) cc_final: 0.7530 (mmm)
REVERT: A  443 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7174 (tp30)
REVERT: A  450 VAL cc_start: 0.7720 (m) cc_final: 0.7429 (p)
REVERT: A  485 ASP cc_start: 0.7640 (m-30) cc_final: 0.7319 (m-30)
REVERT: A  486 ILE cc_start: 0.8458 (mt) cc_final: 0.8069 (mm)
REVERT: A  511 MET cc_start: 0.7709 (tmm) cc_final: 0.7215 (tmm)
REVERT: A  588 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7379 (ttpp)
REVERT: A  628 VAL cc_start: 0.7702 (m) cc_final: 0.7479 (t)
REVERT: A  633 LYS cc_start: 0.8380 (mttt) cc_final: 0.7928 (mmtm)
REVERT: A  634 SER cc_start: 0.8120 (m) cc_final: 0.7730 (p)
REVERT: A  684 ILE cc_start: 0.7156 (mm) cc_final: 0.6681 (pt)
REVERT: A  697 MET cc_start: 0.5659 (tpp) cc_final: 0.5167 (tpp)
REVERT: A  815 LYS cc_start: 0.8403 (tttm) cc_final: 0.8189 (tttp)
REVERT: A  828 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7506 (mmmt)
REVERT: A  841 LYS cc_start: 0.7475 (ttpp) cc_final: 0.7152 (mmtt)
REVERT: A  852 LYS cc_start: 0.8302 (mmtp) cc_final: 0.7843 (mmmm)
REVERT: A  857 MET cc_start: 0.7745 (ttp) cc_final: 0.7366 (ptp)
REVERT: A  876 LEU cc_start: 0.7826 (mt) cc_final: 0.7604 (mm)
REVERT: A  877 GLN cc_start: 0.8006 (mt0) cc_final: 0.7572 (tt0)
REVERT: A  900 GLN cc_start: 0.7997 (mm110) cc_final: 0.7625 (mm-40)
REVERT: A  931 GLU cc_start: 0.7547 (tt0) cc_final: 0.7025 (mt-10)
REVERT: A  961 SER cc_start: 0.8409 (m) cc_final: 0.8080 (p)
REVERT: A  974 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7599 (mtpp)
REVERT: A  999 PHE cc_start: 0.7983 (m-80) cc_final: 0.7719 (m-80)
REVERT: A 1003 SER cc_start: 0.8215 (t) cc_final: 0.7831 (t)
REVERT: A 1104 MET cc_start: 0.7208 (tpp) cc_final: 0.6928 (tpt)
REVERT: A 1118 LYS cc_start: 0.2826 (tmtt) cc_final: 0.1692 (tppt)
REVERT: A 1122 GLU cc_start: 0.7599 (tp30) cc_final: 0.7287 (mt-10)
REVERT: A 1123 ARG cc_start: 0.7482 (mmt180) cc_final: 0.7036 (mmt180)
REVERT: A 1143 GLU cc_start: 0.7227 (tt0) cc_final: 0.6885 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7284 (t0) cc_final: 0.6900 (t0)
REVERT: A 1186 LEU cc_start: 0.8522 (tp) cc_final: 0.8141 (tp)
  outliers start: 25
  outliers final: 22
  residues processed: 227
  average time/residue: 0.2271
  time to fit residues: 68.3590
Evaluate side-chains
  231 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 208
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  629 ASP
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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: 0.7265
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8300  Z= 0.264
  Angle     :  0.502   6.833  11258  Z= 0.261
  Chirality :  0.040   0.242   1354
  Planarity :  0.004   0.051   1379
  Dihedral  :  3.948  25.212   1105
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.57 %
    Favored  : 78.14 %
  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:  1.31 (0.27), residues: 1015
  helix:  1.24 (0.19), residues: 719
  sheet:  1.48 (0.75), residues: 51
  loop : -0.14 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.016   0.001   PHE A 972 
 TYR   0.013   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A1169 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 211
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.7428 (mm) cc_final: 0.7185 (mt)
REVERT: A  120 VAL cc_start: 0.6905 (t) cc_final: 0.6519 (p)
REVERT: A  124 GLU cc_start: 0.7488 (tt0) cc_final: 0.7018 (tm-30)
REVERT: A  140 GLN cc_start: 0.7844 (mp-120) cc_final: 0.7491 (mp10)
REVERT: A  155 ASP cc_start: 0.7775 (t70) cc_final: 0.6972 (t0)
REVERT: A  187 ASN cc_start: 0.7185 (m-40) cc_final: 0.6866 (m-40)
REVERT: A  229 ILE cc_start: 0.7845 (mm) cc_final: 0.7500 (mm)
REVERT: A  320 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7664 (mp0)
REVERT: A  344 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7354 (mm-30)
REVERT: A  355 MET cc_start: 0.7916 (tmm) cc_final: 0.7325 (tmm)
REVERT: A  366 MET cc_start: 0.8139 (mtp) cc_final: 0.7819 (mtp)
REVERT: A  383 MET cc_start: 0.7769 (mmm) cc_final: 0.7445 (mmm)
REVERT: A  443 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7176 (tp30)
REVERT: A  450 VAL cc_start: 0.7724 (m) cc_final: 0.7419 (p)
REVERT: A  485 ASP cc_start: 0.7641 (m-30) cc_final: 0.7298 (m-30)
REVERT: A  500 ARG cc_start: 0.5916 (ttp-170) cc_final: 0.5569 (ttp-170)
REVERT: A  511 MET cc_start: 0.7713 (tmm) cc_final: 0.7210 (tmm)
REVERT: A  588 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7386 (ttpp)
REVERT: A  629 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7666 (m-30)
REVERT: A  633 LYS cc_start: 0.8388 (mttt) cc_final: 0.7937 (mmtm)
REVERT: A  634 SER cc_start: 0.8127 (m) cc_final: 0.7802 (p)
REVERT: A  684 ILE cc_start: 0.7198 (mm) cc_final: 0.6728 (pt)
REVERT: A  697 MET cc_start: 0.5681 (tpp) cc_final: 0.5187 (tpp)
REVERT: A  815 LYS cc_start: 0.8431 (tttm) cc_final: 0.8222 (tttp)
REVERT: A  828 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7612 (mmmt)
REVERT: A  841 LYS cc_start: 0.7532 (ttpp) cc_final: 0.7227 (mmtt)
REVERT: A  852 LYS cc_start: 0.8310 (mmtp) cc_final: 0.7844 (mmmm)
REVERT: A  857 MET cc_start: 0.7770 (ttp) cc_final: 0.7382 (ptp)
REVERT: A  900 GLN cc_start: 0.8018 (mm110) cc_final: 0.7646 (mm-40)
REVERT: A  961 SER cc_start: 0.8438 (m) cc_final: 0.8104 (p)
REVERT: A  974 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7596 (mtpp)
REVERT: A 1003 SER cc_start: 0.8168 (t) cc_final: 0.7784 (t)
REVERT: A 1007 LYS cc_start: 0.7800 (tttt) cc_final: 0.7585 (tttt)
REVERT: A 1118 LYS cc_start: 0.2926 (tmtt) cc_final: 0.1656 (mttm)
REVERT: A 1122 GLU cc_start: 0.7646 (tp30) cc_final: 0.7356 (tt0)
REVERT: A 1123 ARG cc_start: 0.7456 (mmt180) cc_final: 0.6923 (mmt180)
REVERT: A 1143 GLU cc_start: 0.7225 (tt0) cc_final: 0.6874 (mt-10)
REVERT: A 1186 LEU cc_start: 0.8535 (tp) cc_final: 0.8164 (tp)
  outliers start: 29
  outliers final: 23
  residues processed: 230
  average time/residue: 0.2229
  time to fit residues: 68.1503
Evaluate side-chains
  235 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 210
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  629 ASP
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.0070
   chunk 93 optimal weight:    0.5980
   chunk 80 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0170
   chunk 49 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 24 optimal weight:    0.3980
   chunk 74 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.2436

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

Flipped N/Q/H residues before XYZ refinement:
A 726 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8300  Z= 0.135
  Angle     :  0.454   6.002  11258  Z= 0.239
  Chirality :  0.038   0.215   1354
  Planarity :  0.004   0.049   1379
  Dihedral  :  3.778  24.111   1105
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.25 %
    Favored  : 78.14 %
  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:  1.63 (0.27), residues: 1015
  helix:  1.46 (0.19), residues: 717
  sheet:  1.51 (0.76), residues: 51
  loop :  0.05 (0.42), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.005   0.000   HIS A1120 
 PHE   0.011   0.001   PHE A 999 
 TYR   0.007   0.001   TYR A1066 
 ARG   0.004   0.000   ARG A1169 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 215
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.7424 (mm) cc_final: 0.7181 (mt)
REVERT: A  120 VAL cc_start: 0.6858 (t) cc_final: 0.6468 (p)
REVERT: A  124 GLU cc_start: 0.7430 (tt0) cc_final: 0.6986 (tm-30)
REVERT: A  128 ARG cc_start: 0.7505 (ptm160) cc_final: 0.7279 (ptm160)
REVERT: A  140 GLN cc_start: 0.7833 (mp-120) cc_final: 0.7545 (mp10)
REVERT: A  155 ASP cc_start: 0.7835 (t70) cc_final: 0.7002 (t0)
REVERT: A  187 ASN cc_start: 0.7219 (m-40) cc_final: 0.6862 (m-40)
REVERT: A  320 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7703 (mp0)
REVERT: A  344 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7319 (mm-30)
REVERT: A  355 MET cc_start: 0.7886 (tmm) cc_final: 0.7398 (tmm)
REVERT: A  366 MET cc_start: 0.8035 (mtp) cc_final: 0.7633 (mtp)
REVERT: A  377 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7566 (mp)
REVERT: A  383 MET cc_start: 0.7738 (mmm) cc_final: 0.7409 (mmm)
REVERT: A  443 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7156 (tp30)
REVERT: A  450 VAL cc_start: 0.7705 (m) cc_final: 0.7420 (p)
REVERT: A  485 ASP cc_start: 0.7607 (m-30) cc_final: 0.7293 (m-30)
REVERT: A  511 MET cc_start: 0.7714 (tmm) cc_final: 0.7223 (tmm)
REVERT: A  588 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7352 (ttpp)
REVERT: A  633 LYS cc_start: 0.8315 (mttt) cc_final: 0.7858 (mmtm)
REVERT: A  634 SER cc_start: 0.8153 (m) cc_final: 0.7743 (p)
REVERT: A  684 ILE cc_start: 0.7131 (mm) cc_final: 0.6654 (pt)
REVERT: A  697 MET cc_start: 0.5669 (tpp) cc_final: 0.5184 (tpp)
REVERT: A  815 LYS cc_start: 0.8447 (tttm) cc_final: 0.8237 (tttp)
REVERT: A  828 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7486 (mmmt)
REVERT: A  841 LYS cc_start: 0.7448 (ttpp) cc_final: 0.7126 (mmtt)
REVERT: A  852 LYS cc_start: 0.8294 (mmtp) cc_final: 0.7841 (mmmm)
REVERT: A  857 MET cc_start: 0.7772 (ttp) cc_final: 0.7387 (ptp)
REVERT: A  877 GLN cc_start: 0.8130 (tt0) cc_final: 0.7654 (tt0)
REVERT: A  888 GLU cc_start: 0.7622 (tp30) cc_final: 0.7404 (tp30)
REVERT: A  900 GLN cc_start: 0.7984 (mm110) cc_final: 0.7617 (mm-40)
REVERT: A  931 GLU cc_start: 0.7524 (tt0) cc_final: 0.7006 (mt-10)
REVERT: A  961 SER cc_start: 0.8381 (m) cc_final: 0.8056 (p)
REVERT: A  974 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7564 (mtpp)
REVERT: A 1003 SER cc_start: 0.8260 (t) cc_final: 0.7878 (t)
REVERT: A 1007 LYS cc_start: 0.7729 (tttt) cc_final: 0.7454 (tttt)
REVERT: A 1118 LYS cc_start: 0.2861 (tmtt) cc_final: 0.1633 (mttm)
REVERT: A 1122 GLU cc_start: 0.7550 (tp30) cc_final: 0.7295 (tt0)
REVERT: A 1123 ARG cc_start: 0.7530 (mmt180) cc_final: 0.6745 (mmt-90)
REVERT: A 1143 GLU cc_start: 0.7179 (tt0) cc_final: 0.6836 (mt-10)
REVERT: A 1186 LEU cc_start: 0.8511 (tp) cc_final: 0.8156 (tp)
  outliers start: 23
  outliers final: 20
  residues processed: 228
  average time/residue: 0.2170
  time to fit residues: 65.4580
Evaluate side-chains
  232 residues out of total 883 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 210
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  629 ASP
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1100 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 58 optimal weight:    0.4980
   chunk 92 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 832 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.146164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.120215 restraints weight = 11597.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.69
r_work: 0.3338 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8300  Z= 0.235
  Angle     :  0.486   8.217  11258  Z= 0.252
  Chirality :  0.040   0.234   1354
  Planarity :  0.005   0.068   1379
  Dihedral  :  3.850  24.875   1105
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.48 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.27), residues: 1015
  helix:  1.35 (0.19), residues: 721
  sheet:  1.28 (0.74), residues: 53
  loop : -0.11 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.014   0.001   PHE A 972 
 TYR   0.013   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A1169 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2318.67 seconds
wall clock time: 42 minutes 44.95 seconds (2564.95 seconds total)