Starting phenix.real_space_refine
on Mon Jul 28 10:50:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3jd8_6640/07_2025/3jd8_6640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3jd8_6640/07_2025/3jd8_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/cci-nas-00/data/ceres_data/3jd8_6640/07_2025/3jd8_6640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3jd8_6640/07_2025/3jd8_6640.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/3jd8_6640/07_2025/3jd8_6640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3jd8_6640/07_2025/3jd8_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-5711/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: 8.85, per 1000 atoms: 1.10
  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: 2.63
  Conformation dependent library (CDL) restraints added in 1.3 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: 0.89
  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: 2.55

  Time building geometry restraints manager: 2.76 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:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     26.060
  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:3.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.570
-------------------------------------------------------------------------------
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      :  0.021   1.026   8227  Z= 1.084
  Angle     :  2.156  53.458  11319  Z= 1.152
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.34127 (   12)
  link_NAG-ASN         : angle      21.66886 (   36)
  link_ALPHA1-6        : bond        0.00261 (    1)
  link_ALPHA1-6        : angle       0.41226 (    3)
  link_BETA1-4         : bond        0.06807 (    8)
  link_BETA1-4         : angle      12.10249 (   24)
  hydrogen bonds       : bond        0.22692 (  420)
  hydrogen bonds       : angle       9.16474 ( 1206)
  SS BOND              : bond        0.08723 (   11)
  SS BOND              : angle      14.65505 (   22)
  covalent geometry    : bond        0.01542 ( 8195)
  covalent geometry    : angle       1.56376 (11234)

*********************** 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 to be fit.
    rotamer outliers: 76
    poor density    : 248
  time to evaluate  : 0.927 
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: 0.2316
  time to fit residues: 89.8035
Evaluate side-chains
  180 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
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:    3.9990
   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:    2.7990

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.087044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.072162 restraints weight = 48586.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.073182 restraints weight = 37777.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.073970 restraints weight = 31082.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3547
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3547 r_free = 0.3547    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3547 r_free = 0.3547    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.096   8227  Z= 0.273
  Angle     :  1.231  20.720  11319  Z= 0.575
  Chirality :  0.066   0.794   1411
  Planarity :  0.006   0.097   1453
  Dihedral  : 11.725 111.878   1747
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  2.04 %
    Allowed  :  9.49 %
    Favored  : 88.46 %
  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: -1.74 (0.25), residues: 1127
  helix:  0.11 (0.22), residues: 572
  sheet:  0.25 (0.62), residues: 68
  loop : -3.04 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.006   TRP A 381 
 HIS   0.010   0.002   HIS A1042 
 PHE   0.049   0.003   PHE A 760 
 TYR   0.039   0.003   TYR A  56 
 ARG   0.011   0.001   ARG A 161 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01163 (   12)
  link_NAG-ASN         : angle       9.05483 (   36)
  link_ALPHA1-6        : bond        0.00227 (    1)
  link_ALPHA1-6        : angle       2.15998 (    3)
  link_BETA1-4         : bond        0.02547 (    8)
  link_BETA1-4         : angle       4.50743 (   24)
  hydrogen bonds       : bond        0.06459 (  420)
  hydrogen bonds       : angle       5.94806 ( 1206)
  SS BOND              : bond        0.01022 (   11)
  SS BOND              : angle       2.63872 (   22)
  covalent geometry    : bond        0.00584 ( 8195)
  covalent geometry    : angle       1.09812 (11234)

*********************** 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
  192 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 190
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASN cc_start: 0.9297 (m110) cc_final: 0.8869 (m-40)
REVERT: A  544 TRP cc_start: 0.8571 (p90) cc_final: 0.8288 (p90)
REVERT: A  720 LEU cc_start: 0.9495 (mt) cc_final: 0.9207 (mt)
REVERT: A  722 GLN cc_start: 0.9237 (tp40) cc_final: 0.8869 (tm-30)
REVERT: A 1097 ASP cc_start: 0.8724 (m-30) cc_final: 0.8327 (m-30)
REVERT: A 1110 PHE cc_start: 0.8175 (t80) cc_final: 0.7329 (t80)
REVERT: A 1156 ASN cc_start: 0.8510 (t0) cc_final: 0.7915 (t0)
REVERT: A 1168 CYS cc_start: 0.9242 (m) cc_final: 0.8846 (m)
REVERT: A 1170 HIS cc_start: 0.8790 (m90) cc_final: 0.8487 (p-80)
REVERT: A 1225 TYR cc_start: 0.6980 (t80) cc_final: 0.6728 (t80)
REVERT: A 1232 MET cc_start: 0.8063 (ptt) cc_final: 0.7730 (ptt)
  outliers start: 2
  outliers final: 0
  residues processed: 192
  average time/residue: 0.1713
  time to fit residues: 47.3648
Evaluate side-chains
  136 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  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 76 optimal weight:   20.0000
   chunk 83 optimal weight:   20.0000
   chunk 37 optimal weight:    3.9990
   chunk 71 optimal weight:   30.0000
   chunk 107 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 110 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 77 optimal weight:    9.9990
   chunk 26 optimal weight:   30.0000
   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  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 106 ASN
A 150 GLN
A 154 ASN
A 200 GLN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 GLN
A 465 GLN
A 490 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.081727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.066944 restraints weight = 51408.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.067953 restraints weight = 39133.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.068727 restraints weight = 31949.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.5847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.086   8227  Z= 0.269
  Angle     :  1.076  16.421  11319  Z= 0.500
  Chirality :  0.056   0.610   1411
  Planarity :  0.006   0.091   1453
  Dihedral  : 10.312 104.783   1747
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 19.23
  Ramachandran Plot:
    Outliers :  1.33 %
    Allowed  : 10.03 %
    Favored  : 88.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  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: -1.30 (0.25), residues: 1127
  helix:  0.43 (0.22), residues: 583
  sheet: -0.59 (0.59), residues: 78
  loop : -2.67 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.005   TRP A 583 
 HIS   0.012   0.003   HIS A1170 
 PHE   0.037   0.003   PHE A 760 
 TYR   0.024   0.003   TYR A 570 
 ARG   0.023   0.002   ARG A1173 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00840 (   12)
  link_NAG-ASN         : angle       6.76834 (   36)
  link_ALPHA1-6        : bond        0.00292 (    1)
  link_ALPHA1-6        : angle       2.59075 (    3)
  link_BETA1-4         : bond        0.01859 (    8)
  link_BETA1-4         : angle       3.98690 (   24)
  hydrogen bonds       : bond        0.05454 (  420)
  hydrogen bonds       : angle       5.48738 ( 1206)
  SS BOND              : bond        0.00455 (   11)
  SS BOND              : angle       1.62294 (   22)
  covalent geometry    : bond        0.00569 ( 8195)
  covalent geometry    : angle       0.98942 (11234)

*********************** 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
  159 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  390 LEU cc_start: 0.9247 (mp) cc_final: 0.8370 (mt)
REVERT: A  760 PHE cc_start: 0.8393 (m-80) cc_final: 0.7817 (t80)
REVERT: A 1039 MET cc_start: 0.8270 (ppp) cc_final: 0.7549 (mmt)
REVERT: A 1084 PHE cc_start: 0.8354 (p90) cc_final: 0.7913 (p90)
REVERT: A 1097 ASP cc_start: 0.8837 (m-30) cc_final: 0.8483 (m-30)
REVERT: A 1110 PHE cc_start: 0.8752 (t80) cc_final: 0.8450 (t80)
REVERT: A 1128 CYS cc_start: 0.8858 (m) cc_final: 0.7788 (m)
REVERT: A 1159 MET cc_start: 0.8039 (tmm) cc_final: 0.7811 (tmm)
REVERT: A 1168 CYS cc_start: 0.9329 (m) cc_final: 0.8647 (t)
REVERT: A 1170 HIS cc_start: 0.9031 (m90) cc_final: 0.8693 (m90)
REVERT: A 1202 ILE cc_start: 0.8780 (mm) cc_final: 0.8424 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1711
  time to fit residues: 40.0874
Evaluate side-chains
  127 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 110 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 25 optimal weight:   50.0000
   chunk 97 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 68 optimal weight:    9.9990
   chunk 22 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 106 ASN
A 397 GLN
A 452 ASN
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.082096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.067535 restraints weight = 50578.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.068582 restraints weight = 39382.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.069259 restraints weight = 32272.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3466
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.6428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8227  Z= 0.186
  Angle     :  0.971  14.984  11319  Z= 0.446
  Chirality :  0.053   0.546   1411
  Planarity :  0.005   0.074   1453
  Dihedral  :  9.507  90.670   1747
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  1.33 %
    Allowed  :  8.87 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.02 %
    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: -0.85 (0.26), residues: 1127
  helix:  0.77 (0.22), residues: 591
  sheet: -0.95 (0.57), residues: 79
  loop : -2.35 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.007   TRP A 189 
 HIS   0.010   0.002   HIS A1042 
 PHE   0.045   0.002   PHE A 101 
 TYR   0.033   0.002   TYR A 594 
 ARG   0.005   0.001   ARG A1173 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00697 (   12)
  link_NAG-ASN         : angle       6.51345 (   36)
  link_ALPHA1-6        : bond        0.01014 (    1)
  link_ALPHA1-6        : angle       2.83790 (    3)
  link_BETA1-4         : bond        0.01410 (    8)
  link_BETA1-4         : angle       3.72482 (   24)
  hydrogen bonds       : bond        0.04811 (  420)
  hydrogen bonds       : angle       5.24083 ( 1206)
  SS BOND              : bond        0.00519 (   11)
  SS BOND              : angle       1.68910 (   22)
  covalent geometry    : bond        0.00402 ( 8195)
  covalent geometry    : angle       0.88138 (11234)

*********************** 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
  153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.6781 (mmtm) cc_final: 0.6564 (mmtm)
REVERT: A  529 LEU cc_start: 0.8723 (tp) cc_final: 0.8511 (tp)
REVERT: A  722 GLN cc_start: 0.9108 (tp40) cc_final: 0.8693 (tm-30)
REVERT: A 1084 PHE cc_start: 0.8090 (p90) cc_final: 0.7860 (p90)
REVERT: A 1097 ASP cc_start: 0.8773 (m-30) cc_final: 0.8443 (m-30)
REVERT: A 1128 CYS cc_start: 0.8768 (m) cc_final: 0.8288 (m)
REVERT: A 1159 MET cc_start: 0.8194 (tmm) cc_final: 0.7866 (tmm)
REVERT: A 1168 CYS cc_start: 0.8772 (m) cc_final: 0.8439 (t)
REVERT: A 1202 ILE cc_start: 0.8733 (mm) cc_final: 0.8519 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1853
  time to fit residues: 41.5926
Evaluate side-chains
  115 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 109 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:   50.0000
   chunk 99 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 108 optimal weight:    0.7980
   chunk 27 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 110 optimal weight:    8.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.081050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.066483 restraints weight = 50419.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.067459 restraints weight = 39780.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.068146 restraints weight = 32908.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.6973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8227  Z= 0.179
  Angle     :  0.905  14.358  11319  Z= 0.415
  Chirality :  0.050   0.509   1411
  Planarity :  0.005   0.069   1453
  Dihedral  :  8.809  73.354   1747
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  1.24 %
    Allowed  :  8.34 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  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: -0.73 (0.26), residues: 1127
  helix:  0.94 (0.22), residues: 592
  sheet: -1.59 (0.52), residues: 95
  loop : -2.26 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.004   TRP A 189 
 HIS   0.005   0.002   HIS A1170 
 PHE   0.026   0.002   PHE A 760 
 TYR   0.022   0.002   TYR A 594 
 ARG   0.012   0.001   ARG A 116 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00702 (   12)
  link_NAG-ASN         : angle       5.72223 (   36)
  link_ALPHA1-6        : bond        0.01279 (    1)
  link_ALPHA1-6        : angle       3.00698 (    3)
  link_BETA1-4         : bond        0.01290 (    8)
  link_BETA1-4         : angle       3.52128 (   24)
  hydrogen bonds       : bond        0.04427 (  420)
  hydrogen bonds       : angle       5.14531 ( 1206)
  SS BOND              : bond        0.00517 (   11)
  SS BOND              : angle       1.53043 (   22)
  covalent geometry    : bond        0.00381 ( 8195)
  covalent geometry    : angle       0.82901 (11234)

*********************** 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
  148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A  542 PHE cc_start: 0.8350 (m-80) cc_final: 0.8048 (m-80)
REVERT: A  544 TRP cc_start: 0.8640 (p90) cc_final: 0.7727 (p90)
REVERT: A  722 GLN cc_start: 0.9107 (tp40) cc_final: 0.8767 (tm-30)
REVERT: A 1081 TYR cc_start: 0.7513 (t80) cc_final: 0.7227 (t80)
REVERT: A 1101 ASN cc_start: 0.8691 (m-40) cc_final: 0.8465 (m110)
REVERT: A 1128 CYS cc_start: 0.8680 (m) cc_final: 0.8280 (m)
REVERT: A 1159 MET cc_start: 0.8278 (tmm) cc_final: 0.8001 (ppp)
REVERT: A 1168 CYS cc_start: 0.9023 (m) cc_final: 0.8630 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1625
  time to fit residues: 34.9189
Evaluate side-chains
  116 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 76 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 85 optimal weight:   40.0000
   chunk 83 optimal weight:    0.0670
   chunk 33 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 104 optimal weight:    0.9980
   chunk 28 optimal weight:   40.0000
   overall best weight:    4.2124

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
A1137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.079140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.064695 restraints weight = 50045.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.065671 restraints weight = 38766.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.066370 restraints weight = 31887.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3413
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3413
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.7480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8227  Z= 0.204
  Angle     :  0.914  13.732  11319  Z= 0.424
  Chirality :  0.050   0.494   1411
  Planarity :  0.005   0.063   1453
  Dihedral  :  8.308  59.402   1747
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  1.15 %
    Allowed  :  8.70 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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: -0.87 (0.26), residues: 1127
  helix:  0.77 (0.22), residues: 606
  sheet: -1.94 (0.49), residues: 99
  loop : -2.26 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.004   TRP A 583 
 HIS   0.006   0.002   HIS A1170 
 PHE   0.023   0.002   PHE A 603 
 TYR   0.032   0.003   TYR A1229 
 ARG   0.008   0.001   ARG A 116 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00675 (   12)
  link_NAG-ASN         : angle       5.46650 (   36)
  link_ALPHA1-6        : bond        0.01613 (    1)
  link_ALPHA1-6        : angle       2.85053 (    3)
  link_BETA1-4         : bond        0.01221 (    8)
  link_BETA1-4         : angle       3.44179 (   24)
  hydrogen bonds       : bond        0.04519 (  420)
  hydrogen bonds       : angle       5.10140 ( 1206)
  SS BOND              : bond        0.00421 (   11)
  SS BOND              : angle       1.57402 (   22)
  covalent geometry    : bond        0.00432 ( 8195)
  covalent geometry    : angle       0.84425 (11234)

*********************** 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
  139 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
REVERT: A  542 PHE cc_start: 0.8625 (m-80) cc_final: 0.8275 (m-10)
REVERT: A  544 TRP cc_start: 0.8721 (p90) cc_final: 0.7952 (p90)
REVERT: A  586 GLU cc_start: 0.8129 (tp30) cc_final: 0.7878 (tp30)
REVERT: A 1128 CYS cc_start: 0.8744 (m) cc_final: 0.8330 (m)
REVERT: A 1137 ASN cc_start: 0.9189 (m110) cc_final: 0.8775 (m-40)
REVERT: A 1168 CYS cc_start: 0.9088 (m) cc_final: 0.8750 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1712
  time to fit residues: 34.6743
Evaluate side-chains
  116 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 96 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 76 optimal weight:   20.0000
   chunk 93 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 112 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.078370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.063727 restraints weight = 51454.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.064759 restraints weight = 39349.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.065474 restraints weight = 32002.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.8000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8227  Z= 0.215
  Angle     :  0.900  13.486  11319  Z= 0.422
  Chirality :  0.050   0.476   1411
  Planarity :  0.005   0.061   1453
  Dihedral  :  8.060  51.363   1747
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  :  9.32 %
    Favored  : 89.62 %
  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 : 0.19 %

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: -0.83 (0.26), residues: 1127
  helix:  0.86 (0.22), residues: 588
  sheet: -2.11 (0.47), residues: 99
  loop : -2.14 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 544 
 HIS   0.007   0.002   HIS A 398 
 PHE   0.019   0.002   PHE A 760 
 TYR   0.023   0.002   TYR A 594 
 ARG   0.007   0.001   ARG A1173 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00714 (   12)
  link_NAG-ASN         : angle       5.36318 (   36)
  link_ALPHA1-6        : bond        0.01648 (    1)
  link_ALPHA1-6        : angle       2.11232 (    3)
  link_BETA1-4         : bond        0.01141 (    8)
  link_BETA1-4         : angle       3.22837 (   24)
  hydrogen bonds       : bond        0.04472 (  420)
  hydrogen bonds       : angle       5.12807 ( 1206)
  SS BOND              : bond        0.00434 (   11)
  SS BOND              : angle       1.43385 (   22)
  covalent geometry    : bond        0.00454 ( 8195)
  covalent geometry    : angle       0.83506 (11234)

*********************** 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
  133 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 LEU cc_start: 0.8170 (mt) cc_final: 0.7798 (mp)
REVERT: A  475 TYR cc_start: 0.6779 (t80) cc_final: 0.6535 (t80)
REVERT: A  542 PHE cc_start: 0.8565 (m-80) cc_final: 0.8180 (m-10)
REVERT: A  544 TRP cc_start: 0.8720 (p90) cc_final: 0.7871 (p90)
REVERT: A  586 GLU cc_start: 0.8136 (tp30) cc_final: 0.7740 (tp30)
REVERT: A  722 GLN cc_start: 0.9043 (tp40) cc_final: 0.8779 (tm-30)
REVERT: A 1128 CYS cc_start: 0.8688 (m) cc_final: 0.8205 (m)
REVERT: A 1137 ASN cc_start: 0.9216 (m110) cc_final: 0.8737 (m-40)
REVERT: A 1168 CYS cc_start: 0.9086 (m) cc_final: 0.8638 (t)
REVERT: A 1225 TYR cc_start: 0.7649 (t80) cc_final: 0.7040 (t80)
REVERT: A 1228 MET cc_start: 0.9059 (ppp) cc_final: 0.8749 (ppp)
REVERT: A 1233 VAL cc_start: 0.9034 (t) cc_final: 0.8786 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1608
  time to fit residues: 31.1793
Evaluate side-chains
  112 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 87 optimal weight:   30.0000
   chunk 6 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 25 optimal weight:   50.0000
   chunk 106 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 112 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.078522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.063890 restraints weight = 53165.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.064963 restraints weight = 39957.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.065724 restraints weight = 32181.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3369
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.8359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8227  Z= 0.209
  Angle     :  0.914  13.928  11319  Z= 0.427
  Chirality :  0.050   0.466   1411
  Planarity :  0.005   0.060   1453
  Dihedral  :  8.104  51.302   1747
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  9.14 %
    Favored  : 89.97 %
  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: -0.91 (0.26), residues: 1127
  helix:  0.83 (0.22), residues: 587
  sheet: -1.96 (0.48), residues: 100
  loop : -2.29 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 583 
 HIS   0.007   0.002   HIS A 398 
 PHE   0.020   0.002   PHE A 760 
 TYR   0.017   0.002   TYR A 594 
 ARG   0.005   0.001   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00747 (   12)
  link_NAG-ASN         : angle       5.51160 (   36)
  link_ALPHA1-6        : bond        0.01095 (    1)
  link_ALPHA1-6        : angle       2.00380 (    3)
  link_BETA1-4         : bond        0.01055 (    8)
  link_BETA1-4         : angle       3.12177 (   24)
  hydrogen bonds       : bond        0.04465 (  420)
  hydrogen bonds       : angle       5.18859 ( 1206)
  SS BOND              : bond        0.00385 (   11)
  SS BOND              : angle       1.47546 (   22)
  covalent geometry    : bond        0.00440 ( 8195)
  covalent geometry    : angle       0.84763 (11234)

*********************** 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
  129 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: A  542 PHE cc_start: 0.8646 (m-80) cc_final: 0.8179 (m-10)
REVERT: A  544 TRP cc_start: 0.8791 (p90) cc_final: 0.7903 (p90)
REVERT: A  586 GLU cc_start: 0.8277 (tp30) cc_final: 0.7828 (tp30)
REVERT: A  722 GLN cc_start: 0.9038 (tp40) cc_final: 0.8797 (tm-30)
REVERT: A 1101 ASN cc_start: 0.8651 (m-40) cc_final: 0.8394 (m110)
REVERT: A 1128 CYS cc_start: 0.8738 (m) cc_final: 0.8231 (m)
REVERT: A 1137 ASN cc_start: 0.9259 (m110) cc_final: 0.8803 (m110)
REVERT: A 1168 CYS cc_start: 0.9000 (m) cc_final: 0.8716 (t)
REVERT: A 1230 LEU cc_start: 0.8759 (tt) cc_final: 0.8544 (tp)
REVERT: A 1233 VAL cc_start: 0.8949 (t) cc_final: 0.8471 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1728
  time to fit residues: 32.7845
Evaluate side-chains
  112 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 90 optimal weight:   20.0000
   chunk 95 optimal weight:   20.0000
   chunk 100 optimal weight:    0.1980
   chunk 29 optimal weight:    6.9990
   chunk 12 optimal weight:   30.0000
   chunk 9 optimal weight:    6.9990
   chunk 70 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    4.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.077723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.062956 restraints weight = 53353.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.064038 restraints weight = 39639.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.064745 restraints weight = 31758.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3356
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3356
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.8713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   8227  Z= 0.197
  Angle     :  0.887  13.635  11319  Z= 0.416
  Chirality :  0.050   0.449   1411
  Planarity :  0.005   0.059   1453
  Dihedral  :  8.011  58.947   1747
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  9.41 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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: -0.92 (0.26), residues: 1127
  helix:  0.70 (0.22), residues: 606
  sheet: -2.14 (0.47), residues: 98
  loop : -2.18 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 544 
 HIS   0.007   0.002   HIS A 398 
 PHE   0.020   0.002   PHE A 101 
 TYR   0.030   0.002   TYR A 475 
 ARG   0.004   0.001   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00760 (   12)
  link_NAG-ASN         : angle       5.41109 (   36)
  link_ALPHA1-6        : bond        0.00770 (    1)
  link_ALPHA1-6        : angle       1.65182 (    3)
  link_BETA1-4         : bond        0.01016 (    8)
  link_BETA1-4         : angle       2.97460 (   24)
  hydrogen bonds       : bond        0.04379 (  420)
  hydrogen bonds       : angle       5.10645 ( 1206)
  SS BOND              : bond        0.00502 (   11)
  SS BOND              : angle       1.35943 (   22)
  covalent geometry    : bond        0.00420 ( 8195)
  covalent geometry    : angle       0.82244 (11234)

*********************** 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
  124 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A   87 LEU cc_start: 0.9321 (tp) cc_final: 0.9050 (mm)
REVERT: A  542 PHE cc_start: 0.8906 (m-80) cc_final: 0.8447 (m-10)
REVERT: A  544 TRP cc_start: 0.8856 (p90) cc_final: 0.7858 (p90)
REVERT: A  586 GLU cc_start: 0.8509 (tp30) cc_final: 0.8217 (tp30)
REVERT: A  722 GLN cc_start: 0.8960 (tp40) cc_final: 0.8677 (tm-30)
REVERT: A 1101 ASN cc_start: 0.8736 (m-40) cc_final: 0.8428 (m110)
REVERT: A 1128 CYS cc_start: 0.8996 (m) cc_final: 0.8358 (m)
REVERT: A 1137 ASN cc_start: 0.9286 (m110) cc_final: 0.8882 (m-40)
REVERT: A 1168 CYS cc_start: 0.9084 (m) cc_final: 0.8712 (t)
REVERT: A 1230 LEU cc_start: 0.8781 (tt) cc_final: 0.8560 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1704
  time to fit residues: 30.8198
Evaluate side-chains
  105 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
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 27 optimal weight:   20.0000
   chunk 58 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 109 optimal weight:   20.0000
   chunk 89 optimal weight:    0.1980
   chunk 102 optimal weight:    8.9990
   chunk 84 optimal weight:   30.0000
   chunk 12 optimal weight:   20.0000
   overall best weight:    3.6186

-------------------------------------------------------------------------------
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
A 200 GLN
A 486 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.076953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.062601 restraints weight = 51928.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.063620 restraints weight = 39368.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.064341 restraints weight = 31984.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.8990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8227  Z= 0.178
  Angle     :  0.859  13.649  11319  Z= 0.402
  Chirality :  0.049   0.450   1411
  Planarity :  0.005   0.059   1453
  Dihedral  :  7.831  53.028   1747
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  9.41 %
    Favored  : 89.71 %
  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 : 0.19 %

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: -0.90 (0.26), residues: 1127
  helix:  0.70 (0.22), residues: 614
  sheet: -2.12 (0.47), residues: 102
  loop : -2.18 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 544 
 HIS   0.006   0.002   HIS A 398 
 PHE   0.017   0.002   PHE A 760 
 TYR   0.021   0.002   TYR A 475 
 ARG   0.003   0.001   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00812 (   12)
  link_NAG-ASN         : angle       5.27419 (   36)
  link_ALPHA1-6        : bond        0.00740 (    1)
  link_ALPHA1-6        : angle       1.57630 (    3)
  link_BETA1-4         : bond        0.00988 (    8)
  link_BETA1-4         : angle       2.88072 (   24)
  hydrogen bonds       : bond        0.04248 (  420)
  hydrogen bonds       : angle       5.05221 ( 1206)
  SS BOND              : bond        0.00394 (   11)
  SS BOND              : angle       1.45860 (   22)
  covalent geometry    : bond        0.00380 ( 8195)
  covalent geometry    : angle       0.79535 (11234)

********************** 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
  121 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.796 
Fit side-chains
REVERT: A   87 LEU cc_start: 0.9320 (tp) cc_final: 0.9087 (pp)
REVERT: A  586 GLU cc_start: 0.8286 (tp30) cc_final: 0.8061 (tp30)
REVERT: A  722 GLN cc_start: 0.8914 (tp40) cc_final: 0.8682 (tm-30)
REVERT: A 1101 ASN cc_start: 0.8651 (m-40) cc_final: 0.8389 (m110)
REVERT: A 1128 CYS cc_start: 0.8646 (m) cc_final: 0.8087 (m)
REVERT: A 1137 ASN cc_start: 0.9265 (m110) cc_final: 0.8897 (m110)
REVERT: A 1157 LEU cc_start: 0.8901 (mm) cc_final: 0.8687 (mm)
REVERT: A 1168 CYS cc_start: 0.9044 (m) cc_final: 0.8684 (t)
REVERT: A 1230 LEU cc_start: 0.8716 (tt) cc_final: 0.8420 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1514
  time to fit residues: 27.2479
Evaluate side-chains
  101 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 107 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 96 optimal weight:    0.3980
   chunk 54 optimal weight:    3.9990
   chunk 90 optimal weight:   20.0000
   chunk 65 optimal weight:   10.0000
   chunk 68 optimal weight:   20.0000
   overall best weight:    1.8386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.078043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.063245 restraints weight = 51359.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.064335 restraints weight = 38979.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.064912 restraints weight = 31368.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3376
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3376
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.9116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8227  Z= 0.145
  Angle     :  0.832  13.745  11319  Z= 0.384
  Chirality :  0.048   0.446   1411
  Planarity :  0.004   0.059   1453
  Dihedral  :  7.424  54.716   1747
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  8.61 %
    Favored  : 90.59 %
  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: -0.74 (0.26), residues: 1127
  helix:  0.85 (0.22), residues: 611
  sheet: -2.15 (0.47), residues: 98
  loop : -2.11 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 583 
 HIS   0.005   0.001   HIS A 398 
 PHE   0.019   0.001   PHE A 101 
 TYR   0.017   0.002   TYR A 594 
 ARG   0.003   0.001   ARG A 116 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00879 (   12)
  link_NAG-ASN         : angle       5.11056 (   36)
  link_ALPHA1-6        : bond        0.00775 (    1)
  link_ALPHA1-6        : angle       1.42676 (    3)
  link_BETA1-4         : bond        0.01018 (    8)
  link_BETA1-4         : angle       2.73757 (   24)
  hydrogen bonds       : bond        0.03986 (  420)
  hydrogen bonds       : angle       4.85686 ( 1206)
  SS BOND              : bond        0.00326 (   11)
  SS BOND              : angle       1.20163 (   22)
  covalent geometry    : bond        0.00317 ( 8195)
  covalent geometry    : angle       0.77073 (11234)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3093.67 seconds
wall clock time: 55 minutes 51.47 seconds (3351.47 seconds total)