Starting phenix.real_space_refine
on Wed Sep 25 11:53:19 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/09_2024/3jd8_6640.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/09_2024/3jd8_6640.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/09_2024/3jd8_6640.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/09_2024/3jd8_6640.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/09_2024/3jd8_6640.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/09_2024/3jd8_6640.cif"
  }
  resolution = 4.43
  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=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2193 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    5075      2.51       5
     N    1336      2.21       5
     O    1597      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 8050
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 7695
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1133, 7694
          Classifications: {'peptide': 1133}
          Incomplete info: {'truncation_to_alanine': 341}
          Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 56, 'TRANS': 1068}
          Chain breaks: 2
          Unresolved chain link angles: 17
          Unresolved non-hydrogen bonds: 1271
          Unresolved non-hydrogen angles: 1643
          Unresolved non-hydrogen dihedrals: 1110
          Unresolved non-hydrogen chiralities: 105
          Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 9, 'ASP:plan': 20, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 716
      Conformer: "B"
        Number of residues, atoms: 1133, 7694
          Classifications: {'peptide': 1133}
          Incomplete info: {'truncation_to_alanine': 341}
          Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 56, 'TRANS': 1068}
          Chain breaks: 2
          Unresolved chain link angles: 17
          Unresolved non-hydrogen bonds: 1271
          Unresolved non-hydrogen angles: 1643
          Unresolved non-hydrogen dihedrals: 1110
          Unresolved non-hydrogen chiralities: 105
          Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 9, 'ASP:plan': 20, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 716
          bond proxies already assigned to first conformer: 7835
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 182
          Unusual residues: {'CLR': 1, 'NAG': 11}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 11
  Time building chain proxies: 9.18, per 1000 atoms: 1.14
  Number of scatterers: 8050
  At special positions: 0
  Unit cell: (84.9251, 97.9905, 169.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1597      8.00
     N    1336      7.00
     C    5075      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  25 " - pdb=" SG  CYS A  74 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A  42 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  63 " - pdb=" SG  CYS A 109 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 113 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 238 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 160 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 177 " - pdb=" SG  CYS A 184 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A 227 " - pdb=" SG  CYS A 243 " distance=1.91
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 247 " distance=1.79
    Simple disulfide: pdb=" SG  CYS A 468 " - pdb=" SG  CYS A 479 " distance=2.10
    Simple disulfide: pdb=" SG  CYS A 516 " - pdb=" SG  CYS A 533 " distance=2.07

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-6
      " BMA F   3 " - " MAN F   4 "
    BETA1-4
      " NAG A1318 " - " NAG A1319 "
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG A1303 " - " ASN A 158 "
      " NAG A1309 " - " ASN A 572 "
      " NAG A1316 " - " ASN A 122 "
      " NAG A1317 " - " ASN A  70 "
      " NAG A1319 " - " ASN A 185 "
      " NAG A1320 " - " ASN A1064 "
      " NAG A1322 " - " ASN A 135 "
      " NAG A1324 " - " ASN A 459 "
      " NAG B   1 " - " ASN A 222 "
      " NAG C   1 " - " ASN A 524 "
      " NAG D   1 " - " ASN A 557 "
      " NAG E   1 " - " ASN A 598 "
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      53.0% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 54
      No H-bonds generated for 'chain 'A' and resid 52 through 54'
    Processing helix  chain 'A' and resid 55 through 63
    Processing helix  chain 'A' and resid 64 through 67
    Processing helix  chain 'A' and resid 76 through 86
    Processing helix  chain 'A' and resid 87 through 95
    Processing helix  chain 'A' and resid 97 through 114
    Processing helix  chain 'A' and resid 116 through 119
    Processing helix  chain 'A' and resid 149 through 161
    Processing helix  chain 'A' and resid 172 through 177
      removed outlier: 3.599A  pdb=" N   LEU A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 194
    Processing helix  chain 'A' and resid 195 through 199
    Processing helix  chain 'A' and resid 260 through 288
      removed outlier: 3.607A  pdb=" N   GLY A 264 " --> pdb=" O   TRP A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 348
    Processing helix  chain 'A' and resid 351 through 369
    Processing helix  chain 'A' and resid 387 through 400
    Processing helix  chain 'A' and resid 432 through 435
    Processing helix  chain 'A' and resid 436 through 452
    Processing helix  chain 'A' and resid 464 through 468
    Processing helix  chain 'A' and resid 483 through 489
    Processing helix  chain 'A' and resid 491 through 497
    Processing helix  chain 'A' and resid 510 through 517
    Processing helix  chain 'A' and resid 542 through 545
    Processing helix  chain 'A' and resid 554 through 558
    Processing helix  chain 'A' and resid 573 through 594
      removed outlier: 3.534A  pdb=" N   ARG A 579 " --> pdb=" O   GLU A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 617
      removed outlier: 4.051A  pdb=" N   LEU A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASN A 614 " --> pdb=" O   GLU A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 638
      removed outlier: 3.928A  pdb=" N   PHE A 622 " --> pdb=" O   ASP A 618 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   THR A 623 " --> pdb=" O   SER A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 666
      removed outlier: 4.228A  pdb=" N   LEU A 648 " --> pdb=" O   SER A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 698
      removed outlier: 3.645A  pdb=" N   ILE A 678 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      Proline residue:  A 681  - end of helix
      removed outlier: 4.523A  pdb=" N   LEU A 684 " --> pdb=" O   LEU A 680 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ILE A 685 " --> pdb=" O   PRO A 681 " (cutoff:3.500A)
      Proline residue:  A 691  - end of helix
      removed outlier: 3.797A  pdb=" N   VAL A 694 " --> pdb=" O   ILE A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 714
      removed outlier: 3.662A  pdb=" N   TYR A 709 " --> pdb=" O   LEU A 705 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLN A 710 " --> pdb=" O   VAL A 706 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASP A 712 " --> pdb=" O   ALA A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 732
      removed outlier: 3.514A  pdb=" N   ARG A 726 " --> pdb=" O   GLN A 722 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL A 731 " --> pdb=" O   VAL A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 772
      removed outlier: 3.521A  pdb=" N   VAL A 753 " --> pdb=" O   GLY A 749 " (cutoff:3.500A)
      Proline residue:  A 755  - end of helix
      removed outlier: 4.352A  pdb=" N   SER A 761 " --> pdb=" O   VAL A 757 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE A 763 " --> pdb=" O   THR A 759 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA A 764 " --> pdb=" O   PHE A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 830
      Proline residue:  A 827  - end of helix
      removed outlier: 3.982A  pdb=" N   LEU A 830 " --> pdb=" O   SER A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 851
    Processing helix  chain 'A' and resid 864 through 876
    Processing helix  chain 'A' and resid 987 through 995
      removed outlier: 3.527A  pdb=" N   GLN A 991 " --> pdb=" O   LYS A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1005
    Processing helix  chain 'A' and resid 1047 through 1069
      removed outlier: 3.908A  pdb=" N   MET A1069 " --> pdb=" O   VAL A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1089
    Processing helix  chain 'A' and resid 1090 through 1092
      No H-bonds generated for 'chain 'A' and resid 1090 through 1092'
    Processing helix  chain 'A' and resid 1093 through 1113
    Processing helix  chain 'A' and resid 1122 through 1144
      removed outlier: 3.595A  pdb=" N   THR A1130 " --> pdb=" O   ILE A1126 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A1132 " --> pdb=" O   CYS A1128 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A1135 " --> pdb=" O   ILE A1131 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ASN A1137 " --> pdb=" O   MET A1133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1150 through 1174
      removed outlier: 3.828A  pdb=" N   VAL A1155 " --> pdb=" O   ALA A1151 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   HIS A1170 " --> pdb=" O   GLU A1166 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE A1171 " --> pdb=" O   PHE A1167 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA A1174 " --> pdb=" O   HIS A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1184 through 1214
      removed outlier: 3.760A  pdb=" N   GLU A1188 " --> pdb=" O   VAL A1184 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   HIS A1193 " --> pdb=" O   GLU A1189 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A1196 " --> pdb=" O   ALA A1192 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   SER A1197 " --> pdb=" O   HIS A1193 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE A1202 " --> pdb=" O   VAL A1198 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR A1203 " --> pdb=" O   PHE A1199 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   VAL A1211 " --> pdb=" O   PHE A1207 " (cutoff:3.500A)
    Processing sheet with id=A, first strand: chain 'A' and resid 27 through 35
      removed outlier: 6.448A  pdb=" N   GLU A  30 " --> pdb=" O   CYS A  42 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   CYS A  42 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLY A  32 " --> pdb=" O   TYR A  40 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   LYS A  38 " --> pdb=" O   ALA A  34 " (cutoff:3.500A)
    Processing sheet with id=B, first strand: chain 'A' and resid 49 through 50
    Processing sheet with id=C, first strand: chain 'A' and resid 121 through 130
      removed outlier: 6.931A  pdb=" N   LEU A 121 " --> pdb=" O   TYR A 146 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   TYR A 146 " --> pdb=" O   LEU A 121 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL A 123 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LEU A 144 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ALA A 125 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   THR A 204 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 144 " --> pdb=" O   THR A 204 " (cutoff:3.500A)
    Processing sheet with id=D, first strand: chain 'A' and resid 547 through 548
    Processing sheet with id=E, first strand: chain 'A' and resid 418 through 419
    Processing sheet with id=F, first strand: chain 'A' and resid 454 through 457
    Processing sheet with id=G, first strand: chain 'A' and resid 499 through 500
      removed outlier: 6.757A  pdb=" N   LYS A 499 " --> pdb=" O   TYR A 506 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    1206 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: 2.65

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        1.21 -     1.44: 3489
        1.44 -     1.67: 4645
        1.67 -     1.90: 60
        1.90 -     2.13: 0
        2.13 -     2.36: 1
  Bond restraints: 8195
  Sorted by residual:
  bond pdb=" C   VAL A 959 "
       pdb=" N   PRO A 984 "
    ideal  model  delta    sigma   weight residual
    1.334  2.360 -1.026 2.34e-02 1.83e+03 1.92e+03
  bond pdb=" C   SER A 940 "
       pdb=" N   SER A 941 "
    ideal  model  delta    sigma   weight residual
    1.332  1.657 -0.325 1.40e-02 5.10e+03 5.38e+02
  bond pdb=" C   LEU A 469 "
       pdb=" N   ALA A 470 "
    ideal  model  delta    sigma   weight residual
    1.334  1.216  0.118 1.26e-02 6.30e+03 8.77e+01
  bond pdb=" C   LEU A1060 "
       pdb=" N   ILE A1061 "
    ideal  model  delta    sigma   weight residual
    1.334  1.441 -0.107 1.25e-02 6.40e+03 7.33e+01
  bond pdb=" C   GLN A 881 "
       pdb=" N   TYR A 882 "
    ideal  model  delta    sigma   weight residual
    1.331  1.221  0.111 1.33e-02 5.65e+03 6.93e+01
  ... (remaining 8190 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.42: 11153
        6.42 -    12.84: 59
       12.84 -    19.26: 19
       19.26 -    25.67: 2
       25.67 -    32.09: 1
  Bond angle restraints: 11234
  Sorted by residual:
  angle pdb=" CA  VAL A 959 "
        pdb=" C   VAL A 959 "
        pdb=" N   PRO A 984 "
      ideal   model   delta    sigma   weight residual
     118.88   86.79   32.09 1.54e+00 4.22e-01 4.34e+02
  angle pdb=" O   VAL A 959 "
        pdb=" C   VAL A 959 "
        pdb=" N   PRO A 984 "
      ideal   model   delta    sigma   weight residual
     121.10  143.58  -22.48 1.14e+00 7.69e-01 3.89e+02
  angle pdb=" C   VAL A 959 "
        pdb=" N   PRO A 984 "
        pdb=" CA  PRO A 984 "
      ideal   model   delta    sigma   weight residual
     119.84   98.82   21.02 1.25e+00 6.40e-01 2.83e+02
  angle pdb=" N   GLN A 881 "
        pdb=" CA  GLN A 881 "
        pdb=" C   GLN A 881 "
      ideal   model   delta    sigma   weight residual
     108.86  123.53  -14.67 1.41e+00 5.03e-01 1.08e+02
  angle pdb=" N   PHE A 995 "
        pdb=" CA  PHE A 995 "
        pdb=" C   PHE A 995 "
      ideal   model   delta    sigma   weight residual
     108.34  121.88  -13.54 1.31e+00 5.83e-01 1.07e+02
  ... (remaining 11229 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.43: 4839
       24.43 -    48.86: 238
       48.86 -    73.28: 96
       73.28 -    97.71: 23
       97.71 -   122.14: 11
  Dihedral angle restraints: 5207
    sinusoidal: 1924
      harmonic: 3283
  Sorted by residual:
  dihedral pdb=" CB  CYS A 240 "
           pdb=" SG  CYS A 240 "
           pdb=" SG  CYS A 247 "
           pdb=" CB  CYS A 247 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   13.01   79.99     1      1.00e+01 1.00e-02 7.93e+01
  dihedral pdb=" C   SER A 602 "
           pdb=" N   SER A 602 "
           pdb=" CA  SER A 602 "
           pdb=" CB  SER A 602 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -102.74  -19.86     0      2.50e+00 1.60e-01 6.31e+01
  dihedral pdb=" CA  SER A 602 "
           pdb=" C   SER A 602 "
           pdb=" N   PHE A 603 "
           pdb=" CA  PHE A 603 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -142.67  -37.33     0      5.00e+00 4.00e-02 5.57e+01
  ... (remaining 5204 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.409: 1394
       0.409 -    0.817: 10
       0.817 -    1.226: 4
       1.226 -    1.634: 2
       1.634 -    2.043: 1
  Chirality restraints: 1411
  Sorted by residual:
  chirality pdb=" C1  NAG A1318 "
            pdb=" C2  NAG A1318 "
            pdb=" O5  NAG A1318 "
            pdb=" O4  NAG A1319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.84   -1.56 2.00e-02 2.50e+03 6.11e+03
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.87   -1.53 2.00e-02 2.50e+03 5.85e+03
  chirality pdb=" C1  BMA F   3 "
            pdb=" O4  NAG F   2 "
            pdb=" C2  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.96   -0.44 2.00e-02 2.50e+03 4.95e+02
  ... (remaining 1408 not shown)

  Planarity restraints: 1465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 572 "    0.132 2.00e-02 2.50e+03   2.94e-01 1.08e+03
        pdb=" CG  ASN A 572 "   -0.081 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 572 "    0.155 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 572 "   -0.530 2.00e-02 2.50e+03
        pdb=" C1  NAG A1309 "    0.323 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.329 2.00e-02 2.50e+03   2.85e-01 1.02e+03
        pdb=" C7  NAG D   1 "    0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.046 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.501 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.200 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.308 2.00e-02 2.50e+03   2.59e-01 8.41e+02
        pdb=" C7  NAG D   2 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.188 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.446 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1462 not shown)

  Histogram of nonbonded interaction distances:
        1.34 -     2.05: 39
        2.05 -     2.76: 1317
        2.76 -     3.47: 12438
        3.47 -     4.19: 18697
        4.19 -     4.90: 31124
  Nonbonded interactions: 63615
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 942 "
            pdb=" CB  CYS A1011 "
     model   vdw
     1.335 3.440
  nonbonded pdb=" CD2 LEU A 656 "
            pdb=" CB  PRO A 755 "
     model   vdw
     1.371 3.860
  nonbonded pdb=" CG1 VAL A 727 "
            pdb=" CG1 VAL A1165 "
     model   vdw
     1.411 3.880
  nonbonded pdb=" CD2 LEU A 680 "
            pdb=" CE2 TYR A1229 "
     model   vdw
     1.470 3.760
  nonbonded pdb=" O   LEU A 656 "
            pdb=" CD1 LEU A 751 "
     model   vdw
     1.483 3.460
  ... (remaining 63610 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'E'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     26.300
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.060
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
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      :  0.015   1.026   8195  Z= 1.086
  Angle     :  1.564  32.094  11234  Z= 1.019
  Chirality :  0.128   2.043   1411
  Planarity :  0.016   0.285   1453
  Dihedral  : 18.261 122.138   3056
  Min Nonbonded Distance : 1.335

Molprobity Statistics.
  All-atom Clashscore : 78.13
  Ramachandran Plot:
    Outliers :  8.36 %
    Allowed  : 11.91 %
    Favored  : 79.73 %
  Rotamer:
    Outliers : 11.82 %
    Allowed  :  8.55 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.47 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -3.27 (0.23), residues: 1125
  helix: -1.35 (0.20), residues: 546
  sheet: -0.69 (0.56), residues: 85
  loop : -3.45 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP A  27 
 HIS   0.007   0.001   HIS A 441 
 PHE   0.025   0.003   PHE A 203 
 TYR   0.030   0.003   TYR A 147 
 ARG   0.011   0.001   ARG A  78 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 248
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7348 (mttm) cc_final: 0.7017 (mmtm)
REVERT: A  467 ILE cc_start: 0.8263 (pt) cc_final: 0.7808 (mm)
REVERT: A  523 LEU cc_start: 0.7793 (mt) cc_final: 0.7582 (tp)
REVERT: A  541 VAL cc_start: 0.7976 (t) cc_final: 0.7669 (t)
REVERT: A  588 ILE cc_start: 0.8360 (mt) cc_final: 0.7486 (tp)
REVERT: A  678 ILE cc_start: 0.8283 (mt) cc_final: 0.8069 (mt)
REVERT: A  722 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8096 (tm-30)
REVERT: A  760 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8694 (t80)
REVERT: A 1048 SER cc_start: 0.4564 (p) cc_final: 0.3996 (p)
REVERT: A 1072 ASN cc_start: 0.4586 (OUTLIER) cc_final: 0.3909 (t0)
REVERT: A 1094 ILE cc_start: 0.9160 (mm) cc_final: 0.8781 (mm)
  outliers start: 76
  outliers final: 25
  residues processed: 290
  average time/residue: 0.2083
  time to fit residues: 80.0259
Evaluate side-chains
  180 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 85 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 GLN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 GLN
** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 478 ASN
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 HIS
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.4428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.090   8195  Z= 0.396
  Angle     :  1.095  13.837  11234  Z= 0.545
  Chirality :  0.065   0.811   1411
  Planarity :  0.007   0.100   1453
  Dihedral  : 11.731 111.822   1747
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 17.89
  Ramachandran Plot:
    Outliers :  1.95 %
    Allowed  :  9.49 %
    Favored  : 88.55 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.64 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -1.73 (0.25), residues: 1127
  helix:  0.11 (0.22), residues: 571
  sheet:  0.44 (0.63), residues: 66
  loop : -3.03 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.007   TRP A 381 
 HIS   0.009   0.002   HIS A1042 
 PHE   0.049   0.003   PHE A 760 
 TYR   0.038   0.003   TYR A  56 
 ARG   0.010   0.001   ARG A 161 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 191
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7159 (mttm) cc_final: 0.6933 (mptt)
REVERT: A  544 TRP cc_start: 0.7901 (p90) cc_final: 0.7611 (p90)
REVERT: A  632 PHE cc_start: 0.8723 (t80) cc_final: 0.8504 (t80)
REVERT: A  720 LEU cc_start: 0.9020 (mt) cc_final: 0.8707 (mt)
REVERT: A  722 GLN cc_start: 0.9014 (tp40) cc_final: 0.8724 (tm-30)
REVERT: A 1099 ILE cc_start: 0.8701 (mm) cc_final: 0.8375 (mm)
REVERT: A 1156 ASN cc_start: 0.7022 (t0) cc_final: 0.6426 (t0)
REVERT: A 1168 CYS cc_start: 0.7493 (m) cc_final: 0.6760 (m)
REVERT: A 1198 VAL cc_start: 0.8736 (t) cc_final: 0.8495 (t)
REVERT: A 1211 VAL cc_start: 0.9190 (t) cc_final: 0.8774 (t)
REVERT: A 1225 TYR cc_start: 0.6411 (t80) cc_final: 0.6137 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1682
  time to fit residues: 45.9857
Evaluate side-chains
  139 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9980
   chunk 85 optimal weight:   30.0000
   chunk 69 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 102 optimal weight:    8.9990
   chunk 111 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    6.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 GLN
A 465 GLN
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.6097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077   8195  Z= 0.404
  Angle     :  1.034  10.679  11234  Z= 0.507
  Chirality :  0.056   0.604   1411
  Planarity :  0.007   0.093   1453
  Dihedral  : 10.574 106.430   1747
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 20.17
  Ramachandran Plot:
    Outliers :  1.42 %
    Allowed  :  9.76 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.58 (0.25), residues: 1127
  helix:  0.14 (0.21), residues: 589
  sheet: -0.77 (0.58), residues: 79
  loop : -2.75 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.005   TRP A 583 
 HIS   0.012   0.003   HIS A 398 
 PHE   0.037   0.003   PHE A 760 
 TYR   0.032   0.003   TYR A1229 
 ARG   0.014   0.002   ARG A1173 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7360 (mttm) cc_final: 0.7040 (mttt)
REVERT: A  390 LEU cc_start: 0.8690 (mp) cc_final: 0.7869 (mt)
REVERT: A  630 ILE cc_start: 0.9406 (pt) cc_final: 0.9092 (pt)
REVERT: A  632 PHE cc_start: 0.9000 (t80) cc_final: 0.8773 (t80)
REVERT: A  720 LEU cc_start: 0.8993 (mt) cc_final: 0.8773 (mm)
REVERT: A 1084 PHE cc_start: 0.8651 (p90) cc_final: 0.8116 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1586
  time to fit residues: 35.2781
Evaluate side-chains
  121 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0870
   chunk 11 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 69 optimal weight:    0.4980
   chunk 103 optimal weight:    3.9990
   chunk 109 optimal weight:   20.0000
   chunk 97 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 90 optimal weight:   30.0000
   overall best weight:    1.3162

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.6466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8195  Z= 0.246
  Angle     :  0.881  10.043  11234  Z= 0.424
  Chirality :  0.052   0.550   1411
  Planarity :  0.005   0.068   1453
  Dihedral  :  9.534  89.332   1747
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  1.33 %
    Allowed  :  8.52 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.26), residues: 1127
  helix:  0.65 (0.22), residues: 590
  sheet: -1.54 (0.53), residues: 89
  loop : -2.48 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.006   TRP A 189 
 HIS   0.011   0.002   HIS A1042 
 PHE   0.038   0.002   PHE A 101 
 TYR   0.036   0.002   TYR A1037 
 ARG   0.006   0.001   ARG A1173 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7384 (mttm) cc_final: 0.6999 (mttt)
REVERT: A  544 TRP cc_start: 0.8221 (p90) cc_final: 0.6961 (p90)
REVERT: A  630 ILE cc_start: 0.9386 (pt) cc_final: 0.9103 (pt)
REVERT: A  722 GLN cc_start: 0.8698 (tp40) cc_final: 0.8332 (tm-30)
REVERT: A 1191 LEU cc_start: 0.8234 (tp) cc_final: 0.7923 (tt)
REVERT: A 1202 ILE cc_start: 0.8791 (mm) cc_final: 0.7766 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1489
  time to fit residues: 33.8550
Evaluate side-chains
  119 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 93 optimal weight:    7.9990
   chunk 75 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   chunk 55 optimal weight:   20.0000
   chunk 98 optimal weight:    0.8980
   chunk 27 optimal weight:   20.0000
   chunk 36 optimal weight:    8.9990
   overall best weight:    4.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 GLN
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.7106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8195  Z= 0.312
  Angle     :  0.872   9.661  11234  Z= 0.425
  Chirality :  0.051   0.508   1411
  Planarity :  0.005   0.066   1453
  Dihedral  :  9.166  79.218   1747
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  1.33 %
    Allowed  :  8.34 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.26), residues: 1127
  helix:  0.68 (0.22), residues: 588
  sheet: -1.82 (0.51), residues: 89
  loop : -2.15 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.004   TRP A 189 
 HIS   0.008   0.002   HIS A 398 
 PHE   0.024   0.002   PHE A 101 
 TYR   0.032   0.003   TYR A1037 
 ARG   0.010   0.001   ARG A 116 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7475 (mttm) cc_final: 0.7122 (mttt)
REVERT: A 1128 CYS cc_start: 0.8606 (t) cc_final: 0.8357 (p)
REVERT: A 1137 ASN cc_start: 0.7377 (m110) cc_final: 0.6604 (m-40)
REVERT: A 1191 LEU cc_start: 0.8515 (tp) cc_final: 0.8269 (tt)
REVERT: A 1202 ILE cc_start: 0.8842 (mm) cc_final: 0.8256 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1720
  time to fit residues: 36.7805
Evaluate side-chains
  111 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 64 optimal weight:   30.0000
   chunk 26 optimal weight:   40.0000
   chunk 109 optimal weight:   20.0000
   chunk 90 optimal weight:   30.0000
   chunk 50 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 57 optimal weight:   20.0000
   chunk 105 optimal weight:    9.9990
   overall best weight:    6.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1170 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.7990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077   8195  Z= 0.384
  Angle     :  0.951   9.601  11234  Z= 0.473
  Chirality :  0.053   0.488   1411
  Planarity :  0.006   0.063   1453
  Dihedral  :  9.219  64.194   1747
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 20.91
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  :  9.23 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 (0.25), residues: 1127
  helix:  0.30 (0.21), residues: 585
  sheet: -2.59 (0.42), residues: 99
  loop : -2.29 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.004   TRP A 544 
 HIS   0.011   0.002   HIS A 398 
 PHE   0.030   0.003   PHE A 603 
 TYR   0.030   0.003   TYR A 594 
 ARG   0.007   0.001   ARG A 116 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.7540 (mttm) cc_final: 0.7246 (mttt)
REVERT: A  542 PHE cc_start: 0.7294 (m-10) cc_final: 0.7002 (m-80)
REVERT: A  544 TRP cc_start: 0.8154 (p90) cc_final: 0.7218 (p90)
REVERT: A  561 LEU cc_start: 0.7281 (mm) cc_final: 0.7030 (mm)
REVERT: A  630 ILE cc_start: 0.9389 (pt) cc_final: 0.9129 (pt)
REVERT: A  720 LEU cc_start: 0.8516 (pp) cc_final: 0.8192 (pp)
REVERT: A 1039 MET cc_start: 0.7535 (tmm) cc_final: 0.7198 (tmm)
REVERT: A 1102 LEU cc_start: 0.8693 (mt) cc_final: 0.8395 (mt)
REVERT: A 1128 CYS cc_start: 0.8866 (t) cc_final: 0.8522 (p)
REVERT: A 1137 ASN cc_start: 0.7411 (m110) cc_final: 0.6748 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1585
  time to fit residues: 30.4309
Evaluate side-chains
  105 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 79 optimal weight:   20.0000
   chunk 61 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 108 optimal weight:    6.9990
   chunk 68 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 43 optimal weight:   20.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 106 ASN
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 GLN
A1170 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.8383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   8195  Z= 0.315
  Angle     :  0.871   9.495  11234  Z= 0.430
  Chirality :  0.050   0.483   1411
  Planarity :  0.005   0.061   1453
  Dihedral  :  8.540  59.714   1747
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  :  9.05 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.27 (0.25), residues: 1127
  helix:  0.51 (0.22), residues: 587
  sheet: -2.54 (0.44), residues: 101
  loop : -2.30 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP A 189 
 HIS   0.007   0.002   HIS A 398 
 PHE   0.024   0.002   PHE A 603 
 TYR   0.020   0.002   TYR A 594 
 ARG   0.009   0.001   ARG A1173 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.7471 (mttm) cc_final: 0.7189 (mttt)
REVERT: A   87 LEU cc_start: 0.8984 (tp) cc_final: 0.8735 (mm)
REVERT: A  190 ILE cc_start: 0.9122 (mm) cc_final: 0.8801 (mm)
REVERT: A  544 TRP cc_start: 0.7847 (p90) cc_final: 0.6930 (p90)
REVERT: A  561 LEU cc_start: 0.7329 (mm) cc_final: 0.7095 (mm)
REVERT: A 1039 MET cc_start: 0.7478 (tmm) cc_final: 0.6499 (tmm)
REVERT: A 1102 LEU cc_start: 0.8609 (mt) cc_final: 0.8350 (mt)
REVERT: A 1128 CYS cc_start: 0.8857 (t) cc_final: 0.8276 (p)
REVERT: A 1137 ASN cc_start: 0.7644 (m110) cc_final: 0.6867 (m-40)
REVERT: A 1157 LEU cc_start: 0.8291 (mm) cc_final: 0.8023 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1664
  time to fit residues: 29.0599
Evaluate side-chains
  110 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 74 optimal weight:   30.0000
   chunk 53 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 85 optimal weight:    9.9990
   chunk 99 optimal weight:    5.9990
   chunk 104 optimal weight:    0.9990
   chunk 95 optimal weight:   20.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
A 145 GLN
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1170 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.8714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   8195  Z= 0.315
  Angle     :  0.897  14.690  11234  Z= 0.436
  Chirality :  0.050   0.471   1411
  Planarity :  0.005   0.060   1453
  Dihedral  :  8.692  57.398   1747
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  9.58 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.27 (0.26), residues: 1127
  helix:  0.49 (0.22), residues: 590
  sheet: -2.68 (0.43), residues: 113
  loop : -2.20 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 189 
 HIS   0.007   0.002   HIS A 398 
 PHE   0.022   0.002   PHE A 603 
 TYR   0.024   0.002   TYR A 594 
 ARG   0.004   0.001   ARG A 116 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7413 (mttm) cc_final: 0.7149 (mttt)
REVERT: A   87 LEU cc_start: 0.8978 (tp) cc_final: 0.8735 (mm)
REVERT: A  190 ILE cc_start: 0.9159 (mm) cc_final: 0.8846 (mm)
REVERT: A  561 LEU cc_start: 0.7415 (mm) cc_final: 0.7125 (mm)
REVERT: A  630 ILE cc_start: 0.9394 (pt) cc_final: 0.9137 (pt)
REVERT: A 1039 MET cc_start: 0.7493 (tmm) cc_final: 0.6628 (tmm)
REVERT: A 1137 ASN cc_start: 0.7621 (m110) cc_final: 0.6882 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1658
  time to fit residues: 28.9371
Evaluate side-chains
  98 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 91 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 66 optimal weight:    9.9990
   chunk 107 optimal weight:   20.0000
   chunk 65 optimal weight:    0.1980
   overall best weight:    3.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1170 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.8958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   8195  Z= 0.272
  Angle     :  0.847  11.233  11234  Z= 0.413
  Chirality :  0.050   0.468   1411
  Planarity :  0.005   0.060   1453
  Dihedral  :  8.161  52.997   1747
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  9.23 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.26), residues: 1127
  helix:  0.55 (0.22), residues: 596
  sheet: -2.47 (0.48), residues: 81
  loop : -2.17 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 189 
 HIS   0.007   0.002   HIS A1042 
 PHE   0.022   0.002   PHE A 603 
 TYR   0.018   0.002   TYR A 594 
 ARG   0.004   0.001   ARG A 116 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.7374 (mttm) cc_final: 0.7140 (mttt)
REVERT: A   87 LEU cc_start: 0.9019 (tp) cc_final: 0.8795 (mm)
REVERT: A  190 ILE cc_start: 0.9104 (mm) cc_final: 0.8805 (mm)
REVERT: A  193 MET cc_start: 0.8379 (mpp) cc_final: 0.8132 (mpp)
REVERT: A  630 ILE cc_start: 0.9375 (pt) cc_final: 0.9099 (pt)
REVERT: A 1039 MET cc_start: 0.7474 (tmm) cc_final: 0.6434 (tmm)
REVERT: A 1137 ASN cc_start: 0.7569 (m110) cc_final: 0.6787 (m110)
REVERT: A 1171 ILE cc_start: 0.8539 (mm) cc_final: 0.8338 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1640
  time to fit residues: 27.9090
Evaluate side-chains
  96 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 74 optimal weight:   30.0000
   chunk 112 optimal weight:    8.9990
   chunk 103 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0980
   chunk 9 optimal weight:   20.0000
   chunk 69 optimal weight:    0.0770
   chunk 54 optimal weight:    8.9990
   chunk 71 optimal weight:   40.0000
   chunk 95 optimal weight:    8.9990
   chunk 27 optimal weight:   20.0000
   overall best weight:    5.2344

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 ASN
A1170 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.9318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8195  Z= 0.315
  Angle     :  0.881  11.909  11234  Z= 0.429
  Chirality :  0.051   0.450   1411
  Planarity :  0.005   0.064   1453
  Dihedral  :  8.196  50.371   1747
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  9.94 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.26), residues: 1127
  helix:  0.52 (0.22), residues: 593
  sheet: -2.77 (0.46), residues: 89
  loop : -2.13 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.004   TRP A 189 
 HIS   0.007   0.002   HIS A 398 
 PHE   0.027   0.002   PHE A 542 
 TYR   0.022   0.002   TYR A 594 
 ARG   0.005   0.001   ARG A1173 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.7479 (mttm) cc_final: 0.7253 (mttt)
REVERT: A  190 ILE cc_start: 0.9109 (mm) cc_final: 0.8746 (mm)
REVERT: A  630 ILE cc_start: 0.9376 (pt) cc_final: 0.9063 (pt)
REVERT: A 1039 MET cc_start: 0.7370 (tmm) cc_final: 0.6199 (tmm)
REVERT: A 1137 ASN cc_start: 0.7627 (m110) cc_final: 0.6963 (m-40)
REVERT: A 1171 ILE cc_start: 0.8587 (mm) cc_final: 0.8378 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1534
  time to fit residues: 24.9122
Evaluate side-chains
  89 residues out of total 982 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 89 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 78 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 64 optimal weight:   30.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1170 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.075070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.060444 restraints weight = 50551.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.061464 restraints weight = 38265.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.062165 restraints weight = 30868.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.9495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8195  Z= 0.277
  Angle     :  0.839  11.911  11234  Z= 0.409
  Chirality :  0.049   0.461   1411
  Planarity :  0.005   0.059   1453
  Dihedral  :  8.103  56.177   1747
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  9.32 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.25 (0.26), residues: 1127
  helix:  0.48 (0.22), residues: 603
  sheet: -2.73 (0.47), residues: 89
  loop : -2.30 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 189 
 HIS   0.007   0.002   HIS A 398 
 PHE   0.019   0.002   PHE A 587 
 TYR   0.020   0.002   TYR A 594 
 ARG   0.003   0.001   ARG A 116 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1638.96 seconds
wall clock time: 30 minutes 4.34 seconds (1804.34 seconds total)