Starting phenix.real_space_refine
on Wed Sep 17 18:03:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3jd8_6640/09_2025/3jd8_6640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3jd8_6640/09_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_6640/09_2025/3jd8_6640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3jd8_6640/09_2025/3jd8_6640.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/3jd8_6640/09_2025/3jd8_6640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3jd8_6640/09_2025/3jd8_6640.cif"
  }
  resolution = 4.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TRP:plan': 9, 'ASP:plan': 20, 'TYR:plan': 15, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16, 'ASN:plan1': 14, 'HIS:plan': 6, 'GLN:plan1': 14}
          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: {'TRP:plan': 9, 'ASP:plan': 20, 'TYR:plan': 15, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16, 'ASN:plan1': 14, 'HIS:plan': 6, 'GLN:plan1': 14}
          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: 3.40, per 1000 atoms: 0.42
  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: 0.81
  Conformation dependent library (CDL) restraints added in 342.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.21
  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: 1.23

  Time building geometry restraints manager: 1.04 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:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.200
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.290
-------------------------------------------------------------------------------
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 : 78.06
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.011   0.001   ARG A  78 
 TYR   0.030   0.003   TYR A 147 
 PHE   0.025   0.003   PHE A 203 
 TRP   0.021   0.004   TRP A  27 
 HIS   0.007   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.01542 ( 8195)
  covalent geometry    : angle       1.56376 (11234)
  SS BOND              : bond        0.08723 (   11)
  SS BOND              : angle      14.65505 (   22)
  hydrogen bonds       : bond        0.22692 (  420)
  hydrogen bonds       : angle       9.16474 ( 1206)
  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)
  link_NAG-ASN         : bond        0.34127 (   12)
  link_NAG-ASN         : angle      21.66886 (   36)

*********************** 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  : 0.288 
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: 0.0852
  time to fit residues: 33.0628
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  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    2.3186

-------------------------------------------------------------------------------
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
A 154 ASN
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 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 HIS
** A1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.087557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.072531 restraints weight = 49447.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.073589 restraints weight = 38380.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.074385 restraints weight = 31518.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.075010 restraints weight = 27038.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.075428 restraints weight = 23893.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.4424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.093   8227  Z= 0.267
  Angle     :  1.231  21.087  11319  Z= 0.575
  Chirality :  0.065   0.790   1411
  Planarity :  0.007   0.102   1453
  Dihedral  : 11.733 112.113   1747
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  1.95 %
    Allowed  :  9.49 %
    Favored  : 88.55 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.64 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.25), residues: 1127
  helix:  0.11 (0.22), residues: 571
  sheet:  0.49 (0.62), residues: 66
  loop : -3.03 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 161 
 TYR   0.039   0.003   TYR A  56 
 PHE   0.048   0.003   PHE A 760 
 TRP   0.056   0.006   TRP A 381 
 HIS   0.011   0.002   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 8195)
  covalent geometry    : angle       1.09639 (11234)
  SS BOND              : bond        0.00899 (   11)
  SS BOND              : angle       2.60936 (   22)
  hydrogen bonds       : bond        0.06457 (  420)
  hydrogen bonds       : angle       5.94593 ( 1206)
  link_ALPHA1-6        : bond        0.00865 (    1)
  link_ALPHA1-6        : angle       2.30833 (    3)
  link_BETA1-4         : bond        0.01996 (    8)
  link_BETA1-4         : angle       4.65239 (   24)
  link_NAG-ASN         : bond        0.01364 (   12)
  link_NAG-ASN         : angle       9.07262 (   36)

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

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 0.290 
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: A  106 ASN cc_start: 0.9296 (m110) cc_final: 0.8861 (m-40)
REVERT: A  544 TRP cc_start: 0.8554 (p90) cc_final: 0.8332 (p90)
REVERT: A  720 LEU cc_start: 0.9440 (mt) cc_final: 0.9197 (mt)
REVERT: A  722 GLN cc_start: 0.9233 (tp40) cc_final: 0.8884 (tm-30)
REVERT: A 1097 ASP cc_start: 0.8697 (m-30) cc_final: 0.8296 (m-30)
REVERT: A 1156 ASN cc_start: 0.8469 (t0) cc_final: 0.7861 (t0)
REVERT: A 1168 CYS cc_start: 0.9242 (m) cc_final: 0.8836 (m)
REVERT: A 1170 HIS cc_start: 0.8756 (m90) cc_final: 0.8475 (p-80)
REVERT: A 1225 TYR cc_start: 0.6931 (t80) cc_final: 0.6693 (t80)
REVERT: A 1232 MET cc_start: 0.8003 (ptt) cc_final: 0.7670 (ptt)
  outliers start: 1
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0694
  time to fit residues: 19.2353
Evaluate side-chains
  138 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 25 optimal weight:   30.0000
   chunk 83 optimal weight:   20.0000
   chunk 22 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   chunk 105 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 110 optimal weight:    0.0970
   chunk 47 optimal weight:    0.6980
   chunk 67 optimal weight:   40.0000
   overall best weight:    4.1584

-------------------------------------------------------------------------------
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 106 ASN
A 200 GLN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 GLN
A 465 GLN
A 478 ASN
A 490 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.083083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.068399 restraints weight = 50911.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.069388 restraints weight = 39169.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.070181 restraints weight = 32019.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.070711 restraints weight = 27367.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.071159 restraints weight = 24369.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3492
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.5806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   8227  Z= 0.234
  Angle     :  1.050  16.250  11319  Z= 0.484
  Chirality :  0.054   0.619   1411
  Planarity :  0.006   0.088   1453
  Dihedral  : 10.177 102.524   1747
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  1.51 %
    Allowed  :  9.67 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.71 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.26), residues: 1127
  helix:  0.50 (0.22), residues: 587
  sheet: -0.00 (0.65), residues: 68
  loop : -2.73 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1173 
 TYR   0.022   0.003   TYR A 571 
 PHE   0.038   0.003   PHE A 760 
 TRP   0.038   0.004   TRP A 583 
 HIS   0.010   0.002   HIS A1170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 8195)
  covalent geometry    : angle       0.96397 (11234)
  SS BOND              : bond        0.00330 (   11)
  SS BOND              : angle       1.44584 (   22)
  hydrogen bonds       : bond        0.05291 (  420)
  hydrogen bonds       : angle       5.40893 ( 1206)
  link_ALPHA1-6        : bond        0.00500 (    1)
  link_ALPHA1-6        : angle       2.66032 (    3)
  link_BETA1-4         : bond        0.01451 (    8)
  link_BETA1-4         : angle       4.08709 (   24)
  link_NAG-ASN         : bond        0.00767 (   12)
  link_NAG-ASN         : angle       6.58380 (   36)

*********************** 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
  168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  542 PHE cc_start: 0.8565 (m-80) cc_final: 0.8070 (m-80)
REVERT: A  544 TRP cc_start: 0.8842 (p90) cc_final: 0.8208 (p90)
REVERT: A  722 GLN cc_start: 0.9270 (tp40) cc_final: 0.8878 (tm-30)
REVERT: A  760 PHE cc_start: 0.8354 (m-80) cc_final: 0.7746 (t80)
REVERT: A 1039 MET cc_start: 0.8126 (ppp) cc_final: 0.7536 (mmm)
REVERT: A 1084 PHE cc_start: 0.8221 (p90) cc_final: 0.7734 (p90)
REVERT: A 1097 ASP cc_start: 0.8711 (m-30) cc_final: 0.8362 (m-30)
REVERT: A 1110 PHE cc_start: 0.8426 (t80) cc_final: 0.7903 (t80)
REVERT: A 1159 MET cc_start: 0.7955 (tmm) cc_final: 0.7709 (tmm)
REVERT: A 1168 CYS cc_start: 0.9291 (m) cc_final: 0.8603 (t)
REVERT: A 1170 HIS cc_start: 0.8991 (m90) cc_final: 0.8718 (m90)
REVERT: A 1202 ILE cc_start: 0.8733 (mm) cc_final: 0.8251 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0679
  time to fit residues: 16.4956
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  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 105 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 59 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 65 optimal weight:   20.0000
   chunk 45 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   overall best weight:    3.3186

-------------------------------------------------------------------------------
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 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3745 r_free = 0.3745 target = 0.082725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.067774 restraints weight = 52853.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.068954 restraints weight = 39170.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.069753 restraints weight = 31201.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.070372 restraints weight = 26382.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.070851 restraints weight = 23118.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.6411

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= 0.200
  Angle     :  0.973  14.914  11319  Z= 0.446
  Chirality :  0.053   0.552   1411
  Planarity :  0.005   0.072   1453
  Dihedral  :  9.499  89.571   1747
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  1.33 %
    Allowed  :  9.05 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.80 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.26), residues: 1127
  helix:  0.76 (0.22), residues: 590
  sheet: -0.87 (0.57), residues: 79
  loop : -2.37 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 518 
 TYR   0.019   0.002   TYR A1081 
 PHE   0.041   0.002   PHE A 101 
 TRP   0.062   0.004   TRP A 189 
 HIS   0.006   0.002   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 8195)
  covalent geometry    : angle       0.88276 (11234)
  SS BOND              : bond        0.00418 (   11)
  SS BOND              : angle       1.70465 (   22)
  hydrogen bonds       : bond        0.04822 (  420)
  hydrogen bonds       : angle       5.22837 ( 1206)
  link_ALPHA1-6        : bond        0.00863 (    1)
  link_ALPHA1-6        : angle       2.87616 (    3)
  link_BETA1-4         : bond        0.01337 (    8)
  link_BETA1-4         : angle       3.73671 (   24)
  link_NAG-ASN         : bond        0.00672 (   12)
  link_NAG-ASN         : angle       6.52074 (   36)

*********************** 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
  150 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  390 LEU cc_start: 0.9234 (mp) cc_final: 0.8085 (pp)
REVERT: A  529 LEU cc_start: 0.8733 (tp) cc_final: 0.8526 (tp)
REVERT: A  542 PHE cc_start: 0.8712 (m-80) cc_final: 0.8240 (m-80)
REVERT: A  544 TRP cc_start: 0.8737 (p90) cc_final: 0.8342 (p90)
REVERT: A  631 MET cc_start: 0.8895 (ptp) cc_final: 0.8558 (ptp)
REVERT: A  722 GLN cc_start: 0.9099 (tp40) cc_final: 0.8681 (tm-30)
REVERT: A 1041 TYR cc_start: 0.7081 (p90) cc_final: 0.6818 (p90)
REVERT: A 1084 PHE cc_start: 0.8174 (p90) cc_final: 0.7972 (p90)
REVERT: A 1097 ASP cc_start: 0.8768 (m-30) cc_final: 0.8439 (m-30)
REVERT: A 1166 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8832 (tm-30)
REVERT: A 1168 CYS cc_start: 0.8800 (m) cc_final: 0.8523 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 150
  average time/residue: 0.0579
  time to fit residues: 12.8910
Evaluate side-chains
  123 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 99 optimal weight:    0.0270
   chunk 85 optimal weight:   20.0000
   chunk 101 optimal weight:    0.7980
   chunk 29 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 110 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 2 optimal weight:    0.0770
   chunk 62 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    1.9800

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 486 ASN
A 490 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.082013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.067239 restraints weight = 49650.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.068209 restraints weight = 39745.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.068875 restraints weight = 33075.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.069350 restraints weight = 28770.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.069539 restraints weight = 26017.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3480
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3480
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.6940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8227  Z= 0.161
  Angle     :  0.892  14.038  11319  Z= 0.406
  Chirality :  0.049   0.525   1411
  Planarity :  0.005   0.068   1453
  Dihedral  :  8.606  66.563   1747
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  1.33 %
    Allowed  :  7.99 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.26), residues: 1127
  helix:  1.03 (0.22), residues: 589
  sheet: -1.47 (0.52), residues: 91
  loop : -2.31 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 116 
 TYR   0.020   0.002   TYR A 475 
 PHE   0.026   0.002   PHE A 760 
 TRP   0.034   0.003   TRP A 583 
 HIS   0.007   0.001   HIS A1170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8195)
  covalent geometry    : angle       0.81756 (11234)
  SS BOND              : bond        0.00571 (   11)
  SS BOND              : angle       1.47078 (   22)
  hydrogen bonds       : bond        0.04274 (  420)
  hydrogen bonds       : angle       5.02760 ( 1206)
  link_ALPHA1-6        : bond        0.01438 (    1)
  link_ALPHA1-6        : angle       2.82434 (    3)
  link_BETA1-4         : bond        0.01261 (    8)
  link_BETA1-4         : angle       3.43967 (   24)
  link_NAG-ASN         : bond        0.00811 (   12)
  link_NAG-ASN         : angle       5.61427 (   36)

*********************** 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
  154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LEU cc_start: 0.9121 (mt) cc_final: 0.8872 (mt)
REVERT: A  529 LEU cc_start: 0.8654 (tp) cc_final: 0.8429 (tp)
REVERT: A  542 PHE cc_start: 0.8958 (m-80) cc_final: 0.8457 (m-80)
REVERT: A  544 TRP cc_start: 0.8825 (p90) cc_final: 0.8480 (p90)
REVERT: A  586 GLU cc_start: 0.8094 (tp30) cc_final: 0.7855 (tp30)
REVERT: A  722 GLN cc_start: 0.9050 (tp40) cc_final: 0.8690 (tm-30)
REVERT: A 1041 TYR cc_start: 0.6741 (p90) cc_final: 0.6525 (p90)
REVERT: A 1101 ASN cc_start: 0.8691 (m-40) cc_final: 0.8456 (m110)
REVERT: A 1232 MET cc_start: 0.9069 (ppp) cc_final: 0.8850 (ppp)
REVERT: A 1239 HIS cc_start: 0.7533 (t70) cc_final: 0.6973 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0628
  time to fit residues: 14.1668
Evaluate side-chains
  114 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 100 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 64 optimal weight:   20.0000
   chunk 20 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:   30.0000
   chunk 101 optimal weight:    0.0060
   chunk 13 optimal weight:    4.9990
   chunk 17 optimal weight:   20.0000
   overall best weight:    2.2004

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.081442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.066986 restraints weight = 49098.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.067987 restraints weight = 38624.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.068668 restraints weight = 31900.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.069144 restraints weight = 27647.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.069330 restraints weight = 24923.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3479
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.7292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8227  Z= 0.158
  Angle     :  0.860  14.130  11319  Z= 0.394
  Chirality :  0.049   0.500   1411
  Planarity :  0.005   0.064   1453
  Dihedral  :  7.829  52.900   1747
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  :  7.90 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.26), residues: 1127
  helix:  1.03 (0.22), residues: 591
  sheet: -1.87 (0.49), residues: 103
  loop : -2.06 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 116 
 TYR   0.015   0.002   TYR A1081 
 PHE   0.023   0.002   PHE A 760 
 TRP   0.034   0.004   TRP A 189 
 HIS   0.005   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8195)
  covalent geometry    : angle       0.78759 (11234)
  SS BOND              : bond        0.00385 (   11)
  SS BOND              : angle       1.57602 (   22)
  hydrogen bonds       : bond        0.04197 (  420)
  hydrogen bonds       : angle       4.93383 ( 1206)
  link_ALPHA1-6        : bond        0.01727 (    1)
  link_ALPHA1-6        : angle       2.46284 (    3)
  link_BETA1-4         : bond        0.01199 (    8)
  link_BETA1-4         : angle       3.36721 (   24)
  link_NAG-ASN         : bond        0.00800 (   12)
  link_NAG-ASN         : angle       5.41916 (   36)

*********************** 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
  146 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 LEU cc_start: 0.8701 (tp) cc_final: 0.8475 (tp)
REVERT: A  542 PHE cc_start: 0.8959 (m-80) cc_final: 0.8432 (m-80)
REVERT: A  544 TRP cc_start: 0.8810 (p90) cc_final: 0.8418 (p90)
REVERT: A  722 GLN cc_start: 0.8989 (tp40) cc_final: 0.8673 (tm-30)
REVERT: A 1101 ASN cc_start: 0.8661 (m-40) cc_final: 0.8331 (m110)
REVERT: A 1137 ASN cc_start: 0.9083 (m110) cc_final: 0.8608 (m-40)
REVERT: A 1160 SER cc_start: 0.8901 (t) cc_final: 0.8648 (t)
REVERT: A 1170 HIS cc_start: 0.8872 (m-70) cc_final: 0.8338 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0658
  time to fit residues: 14.2841
Evaluate side-chains
  122 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 7 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0020
   chunk 108 optimal weight:    7.9990
   chunk 54 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 83 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0470
   chunk 106 optimal weight:   20.0000
   overall best weight:    3.0092

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** A 407 GLN ** 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 = 0.3714 r_free = 0.3714 target = 0.080200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.065718 restraints weight = 50148.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.066638 restraints weight = 39541.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.067177 restraints weight = 32907.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.067726 restraints weight = 29156.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.068056 restraints weight = 26124.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.7675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8227  Z= 0.168
  Angle     :  0.837  13.963  11319  Z= 0.386
  Chirality :  0.049   0.486   1411
  Planarity :  0.005   0.065   1453
  Dihedral  :  7.410  52.555   1747
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  8.25 %
    Favored  : 90.77 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.26), residues: 1127
  helix:  1.06 (0.22), residues: 603
  sheet: -1.56 (0.52), residues: 90
  loop : -2.22 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 116 
 TYR   0.018   0.002   TYR A1081 
 PHE   0.018   0.002   PHE A 760 
 TRP   0.010   0.002   TRP A 544 
 HIS   0.005   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8195)
  covalent geometry    : angle       0.76991 (11234)
  SS BOND              : bond        0.00386 (   11)
  SS BOND              : angle       1.32338 (   22)
  hydrogen bonds       : bond        0.04098 (  420)
  hydrogen bonds       : angle       4.86754 ( 1206)
  link_ALPHA1-6        : bond        0.01446 (    1)
  link_ALPHA1-6        : angle       2.00362 (    3)
  link_BETA1-4         : bond        0.01033 (    8)
  link_BETA1-4         : angle       3.19699 (   24)
  link_NAG-ASN         : bond        0.00747 (   12)
  link_NAG-ASN         : angle       5.21773 (   36)

*********************** 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  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A  542 PHE cc_start: 0.9041 (m-80) cc_final: 0.8654 (m-80)
REVERT: A  544 TRP cc_start: 0.8873 (p90) cc_final: 0.8388 (p90)
REVERT: A  586 GLU cc_start: 0.8178 (tp30) cc_final: 0.7772 (tp30)
REVERT: A  722 GLN cc_start: 0.8945 (tp40) cc_final: 0.8683 (tm-30)
REVERT: A 1137 ASN cc_start: 0.9089 (m110) cc_final: 0.8587 (m-40)
REVERT: A 1159 MET cc_start: 0.8383 (tmm) cc_final: 0.8116 (ppp)
REVERT: A 1170 HIS cc_start: 0.8867 (m-70) cc_final: 0.8590 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0639
  time to fit residues: 12.4885
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  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 21 optimal weight:   30.0000
   chunk 11 optimal weight:   40.0000
   chunk 49 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 111 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 490 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 = 0.3666 r_free = 0.3666 target = 0.078005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.063365 restraints weight = 51527.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.064400 restraints weight = 39161.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.065095 restraints weight = 31954.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.065616 restraints weight = 27495.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.066003 restraints weight = 24554.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.8140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   8227  Z= 0.230
  Angle     :  0.912  13.878  11319  Z= 0.427
  Chirality :  0.050   0.470   1411
  Planarity :  0.005   0.062   1453
  Dihedral  :  7.805  50.419   1747
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  8.96 %
    Favored  : 90.15 %
  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 : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.26), residues: 1127
  helix:  0.78 (0.22), residues: 604
  sheet: -2.03 (0.47), residues: 101
  loop : -2.13 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 116 
 TYR   0.020   0.002   TYR A1081 
 PHE   0.021   0.002   PHE A 760 
 TRP   0.017   0.003   TRP A 544 
 HIS   0.007   0.002   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 8195)
  covalent geometry    : angle       0.84700 (11234)
  SS BOND              : bond        0.01161 (   11)
  SS BOND              : angle       1.65150 (   22)
  hydrogen bonds       : bond        0.04478 (  420)
  hydrogen bonds       : angle       5.10816 ( 1206)
  link_ALPHA1-6        : bond        0.00921 (    1)
  link_ALPHA1-6        : angle       1.90466 (    3)
  link_BETA1-4         : bond        0.01124 (    8)
  link_BETA1-4         : angle       3.28211 (   24)
  link_NAG-ASN         : bond        0.00783 (   12)
  link_NAG-ASN         : angle       5.33845 (   36)

*********************** 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
  130 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  407 GLN cc_start: 0.8293 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: A  542 PHE cc_start: 0.9118 (m-80) cc_final: 0.8744 (m-80)
REVERT: A  544 TRP cc_start: 0.8960 (p90) cc_final: 0.8340 (p90)
REVERT: A  722 GLN cc_start: 0.8941 (tp40) cc_final: 0.8692 (tm-30)
REVERT: A 1101 ASN cc_start: 0.8561 (m110) cc_final: 0.8290 (m110)
REVERT: A 1137 ASN cc_start: 0.9191 (m110) cc_final: 0.8751 (m-40)
REVERT: A 1159 MET cc_start: 0.8615 (tmm) cc_final: 0.8335 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0678
  time to fit residues: 12.9889
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  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 72 optimal weight:   40.0000
   chunk 71 optimal weight:   20.0000
   chunk 87 optimal weight:   30.0000
   chunk 16 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   chunk 84 optimal weight:   30.0000
   chunk 43 optimal weight:    8.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 ASN
A1101 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.076024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.061531 restraints weight = 54203.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.062629 restraints weight = 40145.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.063370 restraints weight = 32047.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.063890 restraints weight = 27216.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.064257 restraints weight = 24167.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3329
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.8988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083   8227  Z= 0.285
  Angle     :  1.000  13.819  11319  Z= 0.479
  Chirality :  0.054   0.438   1411
  Planarity :  0.006   0.063   1453
  Dihedral  :  8.707  58.932   1747
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 20.72
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  : 10.20 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.26), residues: 1127
  helix:  0.27 (0.21), residues: 594
  sheet: -2.10 (0.47), residues: 102
  loop : -2.26 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 116 
 TYR   0.043   0.003   TYR A1225 
 PHE   0.037   0.003   PHE A 763 
 TRP   0.024   0.003   TRP A 544 
 HIS   0.009   0.002   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 ( 8195)
  covalent geometry    : angle       0.93699 (11234)
  SS BOND              : bond        0.00497 (   11)
  SS BOND              : angle       1.83227 (   22)
  hydrogen bonds       : bond        0.05116 (  420)
  hydrogen bonds       : angle       5.50732 ( 1206)
  link_ALPHA1-6        : bond        0.00571 (    1)
  link_ALPHA1-6        : angle       1.80930 (    3)
  link_BETA1-4         : bond        0.00972 (    8)
  link_BETA1-4         : angle       3.20900 (   24)
  link_NAG-ASN         : bond        0.00848 (   12)
  link_NAG-ASN         : angle       5.58059 (   36)

*********************** 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
  110 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A   87 LEU cc_start: 0.9440 (tp) cc_final: 0.9201 (mm)
REVERT: A  542 PHE cc_start: 0.9184 (m-80) cc_final: 0.8753 (m-80)
REVERT: A  544 TRP cc_start: 0.8808 (p90) cc_final: 0.8055 (p90)
REVERT: A  561 LEU cc_start: 0.8956 (mm) cc_final: 0.8696 (mm)
REVERT: A  760 PHE cc_start: 0.9083 (m-80) cc_final: 0.7955 (t80)
REVERT: A 1101 ASN cc_start: 0.8771 (m-40) cc_final: 0.8453 (m110)
REVERT: A 1137 ASN cc_start: 0.9297 (m110) cc_final: 0.8897 (m-40)
REVERT: A 1159 MET cc_start: 0.8793 (tmm) cc_final: 0.8420 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0687
  time to fit residues: 11.1166
Evaluate side-chains
  94 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 108 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 112 optimal weight:    5.9990
   chunk 87 optimal weight:   30.0000
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 29 optimal weight:   10.0000
   overall best weight:    2.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.077391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.062768 restraints weight = 51047.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.063859 restraints weight = 38014.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.064430 restraints weight = 30429.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.065105 restraints weight = 26363.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.065502 restraints weight = 23198.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.9044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8227  Z= 0.166
  Angle     :  0.900  13.704  11319  Z= 0.420
  Chirality :  0.050   0.449   1411
  Planarity :  0.005   0.063   1453
  Dihedral  :  8.061  55.450   1747
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  8.43 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.26), residues: 1127
  helix:  0.56 (0.22), residues: 593
  sheet: -1.79 (0.52), residues: 88
  loop : -2.22 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 116 
 TYR   0.017   0.002   TYR A 475 
 PHE   0.025   0.002   PHE A 692 
 TRP   0.011   0.002   TRP A 544 
 HIS   0.008   0.002   HIS A1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8195)
  covalent geometry    : angle       0.83864 (11234)
  SS BOND              : bond        0.00372 (   11)
  SS BOND              : angle       1.31604 (   22)
  hydrogen bonds       : bond        0.04452 (  420)
  hydrogen bonds       : angle       5.09108 ( 1206)
  link_ALPHA1-6        : bond        0.00701 (    1)
  link_ALPHA1-6        : angle       1.43857 (    3)
  link_BETA1-4         : bond        0.00931 (    8)
  link_BETA1-4         : angle       2.83521 (   24)
  link_NAG-ASN         : bond        0.00840 (   12)
  link_NAG-ASN         : angle       5.33078 (   36)

********************** 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
  120 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 LEU cc_start: 0.9438 (tp) cc_final: 0.9218 (mm)
REVERT: A  106 ASN cc_start: 0.9326 (p0) cc_final: 0.9065 (p0)
REVERT: A  515 TYR cc_start: 0.8231 (t80) cc_final: 0.7960 (t80)
REVERT: A  542 PHE cc_start: 0.9286 (m-80) cc_final: 0.8958 (m-10)
REVERT: A  722 GLN cc_start: 0.8862 (tp40) cc_final: 0.8625 (tm-30)
REVERT: A 1101 ASN cc_start: 0.8655 (m-40) cc_final: 0.8315 (m110)
REVERT: A 1137 ASN cc_start: 0.9299 (m110) cc_final: 0.8927 (m-40)
REVERT: A 1156 ASN cc_start: 0.9061 (t0) cc_final: 0.8319 (t0)
REVERT: A 1159 MET cc_start: 0.8841 (tmm) cc_final: 0.8636 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0729
  time to fit residues: 12.7437
Evaluate side-chains
  100 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 83 optimal weight:    0.0020
   chunk 64 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 91 optimal weight:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 100 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    3.9996

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
A 200 GLN
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.076477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.061854 restraints weight = 52179.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.062935 restraints weight = 39278.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.063632 restraints weight = 31597.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.064168 restraints weight = 27157.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.064538 restraints weight = 24140.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3363
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.9251

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= 0.194
  Angle     :  0.888  13.431  11319  Z= 0.416
  Chirality :  0.050   0.449   1411
  Planarity :  0.005   0.062   1453
  Dihedral  :  7.819  59.162   1747
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  9.05 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.47 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.26), residues: 1127
  helix:  0.63 (0.22), residues: 598
  sheet: -1.89 (0.52), residues: 88
  loop : -2.14 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 116 
 TYR   0.020   0.002   TYR A1081 
 PHE   0.017   0.002   PHE A 760 
 TRP   0.009   0.002   TRP A 381 
 HIS   0.005   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 8195)
  covalent geometry    : angle       0.82805 (11234)
  SS BOND              : bond        0.00436 (   11)
  SS BOND              : angle       1.26347 (   22)
  hydrogen bonds       : bond        0.04351 (  420)
  hydrogen bonds       : angle       5.07331 ( 1206)
  link_ALPHA1-6        : bond        0.00494 (    1)
  link_ALPHA1-6        : angle       1.59326 (    3)
  link_BETA1-4         : bond        0.00976 (    8)
  link_BETA1-4         : angle       2.89232 (   24)
  link_NAG-ASN         : bond        0.00810 (   12)
  link_NAG-ASN         : angle       5.22639 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1420.41 seconds
wall clock time: 25 minutes 12.95 seconds (1512.95 seconds total)