Starting phenix.real_space_refine
on Wed Mar  4 02:17:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v3f_21035/03_2026/6v3f_21035.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v3f_21035/03_2026/6v3f_21035.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v3f_21035/03_2026/6v3f_21035.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v3f_21035/03_2026/6v3f_21035.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v3f_21035/03_2026/6v3f_21035.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v3f_21035/03_2026/6v3f_21035.cif"
  }
  resolution = 3.7
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    6351      2.51       5
     N    1603      2.21       5
     O    1838      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9855
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 9575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1234, 9575
          Classifications: {'peptide': 1234}
          Link IDs: {'PTRANS': 68, 'TRANS': 1165}
          Chain breaks: 2
    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: 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: "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: "A"
      Number of atoms: 168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 168
          Unusual residues: {'CLR': 1, 'NAG': 10}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
  Time building chain proxies: 2.00, per 1000 atoms: 0.20
  Number of scatterers: 9855
  At special positions: 0
  Unit cell: (99.992, 149.126, 104.302, 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      63     16.00
     O    1838      8.00
     N    1603      7.00
     C    6351      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  32 " - pdb=" SG  CYS A  90 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  38 " - pdb=" SG  CYS A  56 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A 125 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  91 " - pdb=" SG  CYS A 129 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 113 " - pdb=" SG  CYS A 254 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 116 " - pdb=" SG  CYS A 172 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 197 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 243 " - pdb=" SG  CYS A 259 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 256 " - pdb=" SG  CYS A 263 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 471 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 525 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 967 " - pdb=" SG  CYS A1025 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 968 " - pdb=" SG  CYS A 994 " distance=2.03

  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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A1401 " - " ASN A  53 "
      " NAG A1402 " - " ASN A 138 "
      " NAG A1403 " - " ASN A 244 "
      " NAG A1404 " - " ASN A 416 "
      " NAG A1405 " - " ASN A 431 "
      " NAG A1406 " - " ASN A 464 "
      " NAG A1411 " - " ASN A 606 "
      " NAG A1414 " - " ASN A 917 "
      " NAG A1415 " - " ASN A 996 "
      " NAG A1418 " - " ASN A1076 "
      " NAG B   1 " - " ASN A 497 "
      " NAG C   1 " - " ASN A 506 "
      " NAG D   1 " - " ASN A 909 "
      " NAG E   1 " - " ASN A1038 "
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 457.5 milliseconds
  

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2326

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 11 sheets defined
      60.5% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 78 through 81
    Processing helix  chain 'A' and resid 92 through 110
      removed outlier: 4.640A  pdb=" N   ILE A 105 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   THR A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 130
      removed outlier: 3.846A  pdb=" N   SER A 117 " --> pdb=" O   CYS A 113 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ASN A 119 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 135
    Processing helix  chain 'A' and resid 162 through 173
      removed outlier: 4.216A  pdb=" N   CYS A 172 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 188
    Processing helix  chain 'A' and resid 193 through 197
      removed outlier: 3.778A  pdb=" N   CYS A 197 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 208
    Processing helix  chain 'A' and resid 209 through 212
    Processing helix  chain 'A' and resid 255 through 260
    Processing helix  chain 'A' and resid 283 through 313
      removed outlier: 3.770A  pdb=" N   VAL A 294 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER A 299 " --> pdb=" O   PHE A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 351
      removed outlier: 3.521A  pdb=" N   ILE A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TRP A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 368
      removed outlier: 3.658A  pdb=" N   VAL A 355 " --> pdb=" O   TRP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'A' and resid 388 through 402
      removed outlier: 3.509A  pdb=" N   LYS A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 436
    Processing helix  chain 'A' and resid 437 through 454
      removed outlier: 3.713A  pdb=" N   LEU A 441 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU A 443 " --> pdb=" O   ASP A 439 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   HIS A 453 " --> pdb=" O   GLU A 449 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 454 " --> pdb=" O   ARG A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 481 through 485
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 497 through 502
      removed outlier: 3.533A  pdb=" N   MET A 502 " --> pdb=" O   ARG A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 528
      removed outlier: 3.553A  pdb=" N   HIS A 521 " --> pdb=" O   ASP A 517 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASN A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A 528 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 554
    Processing helix  chain 'A' and resid 563 through 567
    Processing helix  chain 'A' and resid 584 through 607
      removed outlier: 3.750A  pdb=" N   GLN A 588 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 632
      removed outlier: 3.818A  pdb=" N   ASN A 626 " --> pdb=" O   GLU A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 651
      removed outlier: 3.638A  pdb=" N   PHE A 636 " --> pdb=" O   ASP A 632 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE A 641 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL A 643 " --> pdb=" O   SER A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 664
    Processing helix  chain 'A' and resid 665 through 691
    Processing helix  chain 'A' and resid 695 through 724
      Proline residue:  A 703  - end of helix
      removed outlier: 3.962A  pdb=" N   VAL A 709 " --> pdb=" O   LEU A 705 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ASP A 712 " --> pdb=" O   ALA A 708 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ASN A 713 " --> pdb=" O   VAL A 709 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ILE A 714 " --> pdb=" O   GLY A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 762
      Proline residue:  A 745  - end of helix
      removed outlier: 3.762A  pdb=" N   ALA A 762 " --> pdb=" O   PHE A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 788
      removed outlier: 3.685A  pdb=" N   ILE A 781 " --> pdb=" O   GLY A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 804
      removed outlier: 3.579A  pdb=" N   ALA A 804 " --> pdb=" O   LYS A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 835
    Processing helix  chain 'A' and resid 835 through 841
      removed outlier: 3.696A  pdb=" N   PHE A 839 " --> pdb=" O   ILE A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 864
    Processing helix  chain 'A' and resid 872 through 877
      removed outlier: 3.556A  pdb=" N   LEU A 875 " --> pdb=" O   ASP A 872 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU A 877 " --> pdb=" O   GLU A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 894
      removed outlier: 4.344A  pdb=" N   ASP A 885 " --> pdb=" O   SER A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 918
    Processing helix  chain 'A' and resid 929 through 938
    Processing helix  chain 'A' and resid 952 through 962
    Processing helix  chain 'A' and resid 963 through 966
    Processing helix  chain 'A' and resid 1005 through 1017
      Proline residue:  A1014  - end of helix
    Processing helix  chain 'A' and resid 1059 through 1082
    Processing helix  chain 'A' and resid 1099 through 1104
      removed outlier: 3.531A  pdb=" N   TYR A1103 " --> pdb=" O   SER A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1105 through 1107
      No H-bonds generated for 'chain 'A' and resid 1105 through 1107'
    Processing helix  chain 'A' and resid 1112 through 1120
      removed outlier: 4.584A  pdb=" N   THR A1116 " --> pdb=" O   GLU A1112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1121 through 1132
      removed outlier: 3.963A  pdb=" N   PHE A1125 " --> pdb=" O   PHE A1121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1135 through 1160
      removed outlier: 3.574A  pdb=" N   GLY A1139 " --> pdb=" O   ASP A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1165 through 1179
    Processing helix  chain 'A' and resid 1179 through 1192
      removed outlier: 4.848A  pdb=" N   HIS A1185 " --> pdb=" O   GLU A1181 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   ILE A1186 " --> pdb=" O   PHE A1182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1197 through 1227
      removed outlier: 3.652A  pdb=" N   LYS A1203 " --> pdb=" O   LEU A1199 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASP A1204 " --> pdb=" O   GLU A1200 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA A1205 " --> pdb=" O   ARG A1201 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   MET A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
      Proline residue:  A1223  - end of helix
      removed outlier: 3.780A  pdb=" N   ILE A1227 " --> pdb=" O   PRO A1223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1228 through 1231
    Processing helix  chain 'A' and resid 1233 through 1240
    Processing helix  chain 'A' and resid 1240 through 1257
    Processing helix  chain 'A' and resid 1257 through 1267
      removed outlier: 3.868A  pdb=" N   VAL A1261 " --> pdb=" O   VAL A1257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1271 through 1281
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37
      removed outlier: 5.273A  pdb=" N   GLU A  36 " --> pdb=" O   CYS A  56 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   CYS A  56 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64
    Processing sheet with id=AA3, first strand: chain 'A' and resid 137 through 139
    Processing sheet with id=AA4, first strand: chain 'A' and resid 277 through 278
    Processing sheet with id=AA5, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA7, first strand: chain 'A' and resid 420 through 424
    Processing sheet with id=AA8, first strand: chain 'A' and resid 456 through 458
    Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 509
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1037 through 1039
      removed outlier: 6.993A  pdb=" N   ASN A1038 " --> pdb=" O   ILE A1046 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 980 through 981
      removed outlier: 4.442A  pdb=" N   ARG A 969 " --> pdb=" O   CYS A 981 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS A 992 " --> pdb=" O   LEU A 970 " (cutoff:3.500A)

    527 hydrogen bonds defined for protein.
    1482 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: 1.67

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 3080
        1.35 -     1.47: 2555
        1.47 -     1.60: 4364
        1.60 -     1.72: 0
        1.72 -     1.85: 87
  Bond restraints: 10086
  Sorted by residual:
  bond pdb=" C1  NAG A1404 "
       pdb=" O5  NAG A1404 "
    ideal  model  delta    sigma   weight residual
    1.406  1.462 -0.056 2.00e-02 2.50e+03 7.73e+00
  bond pdb=" C17 CLR A1419 "
       pdb=" C20 CLR A1419 "
    ideal  model  delta    sigma   weight residual
    1.535  1.590 -0.055 2.00e-02 2.50e+03 7.52e+00
  bond pdb=" C1  NAG A1403 "
       pdb=" O5  NAG A1403 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.64e+00
  bond pdb=" C1  NAG A1405 "
       pdb=" O5  NAG A1405 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.54e+00
  bond pdb=" C1  NAG A1411 "
       pdb=" O5  NAG A1411 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.34e+00
  ... (remaining 10081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.60: 13517
        3.60 -     7.21: 185
        7.21 -    10.81: 27
       10.81 -    14.42: 6
       14.42 -    18.02: 1
  Bond angle restraints: 13736
  Sorted by residual:
  angle pdb=" CA  CYS A 113 "
        pdb=" CB  CYS A 113 "
        pdb=" SG  CYS A 113 "
      ideal   model   delta    sigma   weight residual
     114.40  127.59  -13.19 2.30e+00 1.89e-01 3.29e+01
  angle pdb=" CA  LEU A  48 "
        pdb=" CB  LEU A  48 "
        pdb=" CG  LEU A  48 "
      ideal   model   delta    sigma   weight residual
     116.30  134.32  -18.02 3.50e+00 8.16e-02 2.65e+01
  angle pdb=" C   HIS A 453 "
        pdb=" N   LEU A 454 "
        pdb=" CA  LEU A 454 "
      ideal   model   delta    sigma   weight residual
     121.31  128.66   -7.35 1.49e+00 4.50e-01 2.44e+01
  angle pdb=" C   SER A 655 "
        pdb=" N   ARG A 656 "
        pdb=" CA  ARG A 656 "
      ideal   model   delta    sigma   weight residual
     121.54  130.89   -9.35 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" C   ALA A 228 "
        pdb=" N   LEU A 229 "
        pdb=" CA  LEU A 229 "
      ideal   model   delta    sigma   weight residual
     121.80  133.55  -11.75 2.44e+00 1.68e-01 2.32e+01
  ... (remaining 13731 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 5933
       17.21 -    34.42: 288
       34.42 -    51.62: 73
       51.62 -    68.83: 26
       68.83 -    86.04: 5
  Dihedral angle restraints: 6325
    sinusoidal: 2726
      harmonic: 3599
  Sorted by residual:
  dihedral pdb=" CB  CYS A  38 "
           pdb=" SG  CYS A  38 "
           pdb=" SG  CYS A  56 "
           pdb=" CB  CYS A  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.22   85.22     1      1.00e+01 1.00e-02 8.80e+01
  dihedral pdb=" CB  CYS A 243 "
           pdb=" SG  CYS A 243 "
           pdb=" SG  CYS A 259 "
           pdb=" CB  CYS A 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.01  -65.01     1      1.00e+01 1.00e-02 5.54e+01
  dihedral pdb=" CB  CYS A  77 "
           pdb=" SG  CYS A  77 "
           pdb=" SG  CYS A 125 "
           pdb=" CB  CYS A 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.19  -47.19     1      1.00e+01 1.00e-02 3.08e+01
  ... (remaining 6322 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 1541
       0.124 -    0.248: 93
       0.248 -    0.372: 5
       0.372 -    0.496: 1
       0.496 -    0.620: 1
  Chirality restraints: 1641
  Sorted by residual:
  chirality pdb=" C1  NAG A1404 "
            pdb=" ND2 ASN A 416 "
            pdb=" C2  NAG A1404 "
            pdb=" O5  NAG A1404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.78   -0.62 2.00e-01 2.50e+01 9.60e+00
  chirality pdb=" C1  NAG A1405 "
            pdb=" ND2 ASN A 431 "
            pdb=" C2  NAG A1405 "
            pdb=" O5  NAG A1405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.19e+00
  chirality pdb=" C2  NAG D   2 "
            pdb=" C1  NAG D   2 "
            pdb=" C3  NAG D   2 "
            pdb=" N2  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.13   -0.36 2.00e-01 2.50e+01 3.20e+00
  ... (remaining 1638 not shown)

  Planarity restraints: 1738
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 113 "   -0.019 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" C   CYS A 113 "    0.064 2.00e-02 2.50e+03
        pdb=" O   CYS A 113 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   PRO A 114 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 126 "   -0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   HIS A 126 "    0.060 2.00e-02 2.50e+03
        pdb=" O   HIS A 126 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ASN A 127 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 286 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   ALA A 286 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ALA A 286 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   LEU A 287 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1735 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2377
        2.81 -     3.33: 9256
        3.33 -     3.85: 15447
        3.85 -     4.38: 16574
        4.38 -     4.90: 30061
  Nonbonded interactions: 73715
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 108 "
            pdb=" OG1 THR A 111 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   ASN A 119 "
            pdb=" OG  SER A 122 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" N   ASP A 872 "
            pdb=" OD1 ASP A 872 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OG  SER A 437 "
            pdb=" OD1 ASP A 439 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OD2 ASP A 956 "
            pdb=" OH  TYR A1033 "
     model   vdw
     2.319 3.040
  ... (remaining 73710 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 'D'
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.370
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
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      :  0.007   0.091  10117  Z= 0.327
  Angle     :  1.215  18.024  13816  Z= 0.661
  Chirality :  0.067   0.620   1641
  Planarity :  0.008   0.044   1724
  Dihedral  : 11.527  86.038   3960
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.44 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  4.16 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.23), residues: 1228
  helix:  1.42 (0.19), residues: 628
  sheet:  0.70 (0.57), residues: 80
  loop :  0.04 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  79 
 TYR   0.031   0.003   TYR A 689 
 PHE   0.022   0.003   PHE A 411 
 TRP   0.050   0.003   TRP A 202 
 HIS   0.010   0.003   HIS A 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00666 (10086)
  covalent geometry    : angle       1.17730 (13736)
  SS BOND              : bond        0.00804 (   13)
  SS BOND              : angle       3.09272 (   26)
  hydrogen bonds       : bond        0.19026 (  525)
  hydrogen bonds       : angle       6.81119 ( 1482)
  link_BETA1-4         : bond        0.01290 (    4)
  link_BETA1-4         : angle       6.22055 (   12)
  link_NAG-ASN         : bond        0.00580 (   14)
  link_NAG-ASN         : angle       3.91646 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 HIS cc_start: 0.7794 (m-70) cc_final: 0.7578 (m-70)
REVERT: A  156 TYR cc_start: 0.8362 (p90) cc_final: 0.7938 (p90)
REVERT: A  290 ILE cc_start: 0.8637 (mm) cc_final: 0.8431 (mt)
REVERT: A 1144 LEU cc_start: 0.9010 (mt) cc_final: 0.8795 (mt)
REVERT: A 1148 MET cc_start: 0.8534 (mtp) cc_final: 0.8313 (mtp)
  outliers start: 11
  outliers final: 8
  residues processed: 146
  average time/residue: 0.1092
  time to fit residues: 21.9393
Evaluate side-chains
  83 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  872 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 ASN
** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 631 GLN
A 860 ASN
A1010 HIS
A1234 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.117703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.085879 restraints weight = 18724.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.086428 restraints weight = 13379.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.086898 restraints weight = 12554.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.088711 restraints weight = 8781.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.088575 restraints weight = 6878.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10117  Z= 0.174
  Angle     :  0.746  11.329  13816  Z= 0.369
  Chirality :  0.045   0.269   1641
  Planarity :  0.005   0.044   1724
  Dihedral  :  7.467  59.089   1783
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.12 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  8.70 %
    Favored  : 89.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  1.43 (0.23), residues: 1228
  helix:  1.87 (0.19), residues: 634
  sheet:  0.39 (0.57), residues: 80
  loop : -0.05 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  75 
 TYR   0.019   0.002   TYR A 646 
 PHE   0.018   0.002   PHE A 291 
 TRP   0.030   0.002   TRP A 202 
 HIS   0.003   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (10086)
  covalent geometry    : angle       0.72196 (13736)
  SS BOND              : bond        0.00361 (   13)
  SS BOND              : angle       1.51948 (   26)
  hydrogen bonds       : bond        0.07153 (  525)
  hydrogen bonds       : angle       5.32731 ( 1482)
  link_BETA1-4         : bond        0.00953 (    4)
  link_BETA1-4         : angle       3.56458 (   12)
  link_NAG-ASN         : bond        0.00356 (   14)
  link_NAG-ASN         : angle       2.76779 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A 1148 MET cc_start: 0.8496 (mtp) cc_final: 0.7908 (mtp)
REVERT: A 1152 ASP cc_start: 0.8320 (m-30) cc_final: 0.8113 (m-30)
  outliers start: 15
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0672
  time to fit residues: 10.7142
Evaluate side-chains
  79 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  206 GLN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  867 ILE
Chi-restraints excluded: chain A residue 1130 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 118 optimal weight:    4.9990
   chunk 46 optimal weight:    0.3980
   chunk 87 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 97 optimal weight:    0.3980
   chunk 89 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 21 optimal weight:    0.4980
   overall best weight:    1.4382

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

Flipped N/Q/H residues before XYZ refinement:
A 126 HIS
A 860 ASN
A1010 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.117842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.087234 restraints weight = 18768.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.086633 restraints weight = 12897.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.087331 restraints weight = 13933.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.087953 restraints weight = 9088.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.088511 restraints weight = 7954.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10117  Z= 0.141
  Angle     :  0.666  14.867  13816  Z= 0.324
  Chirality :  0.043   0.261   1641
  Planarity :  0.004   0.045   1724
  Dihedral  :  6.816  57.824   1778
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.77 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  9.18 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  1.39 (0.24), residues: 1228
  helix:  1.86 (0.20), residues: 639
  sheet:  0.38 (0.57), residues: 80
  loop : -0.14 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 726 
 TYR   0.020   0.001   TYR A 936 
 PHE   0.014   0.001   PHE A 411 
 TRP   0.023   0.001   TRP A 202 
 HIS   0.011   0.002   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10086)
  covalent geometry    : angle       0.64579 (13736)
  SS BOND              : bond        0.00326 (   13)
  SS BOND              : angle       1.17617 (   26)
  hydrogen bonds       : bond        0.05780 (  525)
  hydrogen bonds       : angle       4.96660 ( 1482)
  link_BETA1-4         : bond        0.01080 (    4)
  link_BETA1-4         : angle       3.45252 (   12)
  link_NAG-ASN         : bond        0.00334 (   14)
  link_NAG-ASN         : angle       2.24768 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7997 (mpt180) cc_final: 0.7564 (mpt180)
REVERT: A   94 LYS cc_start: 0.8459 (mmmt) cc_final: 0.7698 (tmtt)
REVERT: A  287 LEU cc_start: 0.8276 (tt) cc_final: 0.8057 (tp)
REVERT: A 1148 MET cc_start: 0.8485 (mtp) cc_final: 0.7959 (mtp)
  outliers start: 21
  outliers final: 12
  residues processed: 99
  average time/residue: 0.0697
  time to fit residues: 10.9157
Evaluate side-chains
  84 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  126 HIS
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1253 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0870
   chunk 48 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 59 optimal weight:    0.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
A 126 HIS
A1010 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.117311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.086435 restraints weight = 18873.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.087765 restraints weight = 13691.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.087839 restraints weight = 13966.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.088599 restraints weight = 8516.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.090097 restraints weight = 7315.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10117  Z= 0.143
  Angle     :  0.640  13.679  13816  Z= 0.312
  Chirality :  0.043   0.260   1641
  Planarity :  0.004   0.042   1724
  Dihedral  :  6.528  57.289   1776
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.93 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.27 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  1.39 (0.24), residues: 1228
  helix:  1.87 (0.20), residues: 642
  sheet:  0.19 (0.58), residues: 80
  loop : -0.13 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  63 
 TYR   0.016   0.001   TYR A 646 
 PHE   0.013   0.001   PHE A 411 
 TRP   0.015   0.001   TRP A 202 
 HIS   0.012   0.002   HIS A 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10086)
  covalent geometry    : angle       0.62152 (13736)
  SS BOND              : bond        0.00433 (   13)
  SS BOND              : angle       1.28072 (   26)
  hydrogen bonds       : bond        0.05618 (  525)
  hydrogen bonds       : angle       4.89516 ( 1482)
  link_BETA1-4         : bond        0.01008 (    4)
  link_BETA1-4         : angle       3.39786 (   12)
  link_NAG-ASN         : bond        0.00287 (   14)
  link_NAG-ASN         : angle       2.05808 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7937 (mpt180) cc_final: 0.7589 (mpt180)
REVERT: A   94 LYS cc_start: 0.8427 (mmmt) cc_final: 0.7662 (tmtt)
REVERT: A 1148 MET cc_start: 0.8410 (mtp) cc_final: 0.8172 (mtp)
  outliers start: 23
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0700
  time to fit residues: 10.1067
Evaluate side-chains
  92 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  632 ASP
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  867 ILE
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1253 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0770
   chunk 103 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    1.3742

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS
A 626 ASN
A1010 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.117645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.087158 restraints weight = 18786.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.086167 restraints weight = 12970.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.086890 restraints weight = 14714.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.087603 restraints weight = 9060.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.089130 restraints weight = 7852.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10117  Z= 0.128
  Angle     :  0.611  13.095  13816  Z= 0.295
  Chirality :  0.042   0.256   1641
  Planarity :  0.004   0.037   1724
  Dihedral  :  6.289  56.798   1776
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.18 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 10.12 %
    Favored  : 87.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  1.46 (0.24), residues: 1228
  helix:  1.92 (0.20), residues: 645
  sheet:  0.27 (0.57), residues: 78
  loop : -0.11 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  75 
 TYR   0.017   0.001   TYR A 646 
 PHE   0.013   0.001   PHE A 717 
 TRP   0.014   0.001   TRP A 202 
 HIS   0.006   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10086)
  covalent geometry    : angle       0.59388 (13736)
  SS BOND              : bond        0.00281 (   13)
  SS BOND              : angle       1.03282 (   26)
  hydrogen bonds       : bond        0.05185 (  525)
  hydrogen bonds       : angle       4.77660 ( 1482)
  link_BETA1-4         : bond        0.01002 (    4)
  link_BETA1-4         : angle       3.34895 (   12)
  link_NAG-ASN         : bond        0.00264 (   14)
  link_NAG-ASN         : angle       1.87025 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8489 (mmmt) cc_final: 0.7696 (tmtt)
REVERT: A  717 PHE cc_start: 0.9283 (t80) cc_final: 0.9058 (t80)
REVERT: A 1148 MET cc_start: 0.8392 (mtp) cc_final: 0.8171 (mtp)
REVERT: A 1253 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8668 (mm)
  outliers start: 25
  outliers final: 16
  residues processed: 96
  average time/residue: 0.0713
  time to fit residues: 10.7751
Evaluate side-chains
  89 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue 1109 VAL
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1253 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 15 optimal weight:   20.0000
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A1010 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.116338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.085435 restraints weight = 18992.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.084689 restraints weight = 13039.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.085503 restraints weight = 14359.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.086017 restraints weight = 9108.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.086506 restraints weight = 8044.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10117  Z= 0.155
  Angle     :  0.642  12.430  13816  Z= 0.308
  Chirality :  0.043   0.263   1641
  Planarity :  0.004   0.036   1724
  Dihedral  :  6.230  57.059   1775
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.58 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 10.88 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  1.39 (0.24), residues: 1228
  helix:  1.90 (0.20), residues: 644
  sheet:  0.22 (0.57), residues: 78
  loop : -0.20 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 417 
 TYR   0.016   0.002   TYR A 646 
 PHE   0.013   0.001   PHE A 411 
 TRP   0.011   0.001   TRP A 960 
 HIS   0.004   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (10086)
  covalent geometry    : angle       0.62680 (13736)
  SS BOND              : bond        0.00265 (   13)
  SS BOND              : angle       1.00898 (   26)
  hydrogen bonds       : bond        0.05467 (  525)
  hydrogen bonds       : angle       4.78473 ( 1482)
  link_BETA1-4         : bond        0.00965 (    4)
  link_BETA1-4         : angle       3.33489 (   12)
  link_NAG-ASN         : bond        0.00242 (   14)
  link_NAG-ASN         : angle       1.82733 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8524 (mmmt) cc_final: 0.7740 (tmtt)
REVERT: A  586 MET cc_start: 0.7861 (mmm) cc_final: 0.7515 (tpp)
REVERT: A 1148 MET cc_start: 0.8395 (mtp) cc_final: 0.8189 (mtp)
  outliers start: 24
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0740
  time to fit residues: 10.3847
Evaluate side-chains
  90 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue 1109 VAL
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1217 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 106 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 90 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 49 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 860 ASN
A1010 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.117395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.086509 restraints weight = 18896.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.085812 restraints weight = 13162.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.086678 restraints weight = 14391.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.087159 restraints weight = 9056.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.087679 restraints weight = 8020.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10117  Z= 0.125
  Angle     :  0.623  12.572  13816  Z= 0.296
  Chirality :  0.042   0.255   1641
  Planarity :  0.004   0.036   1724
  Dihedral  :  6.079  56.843   1775
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.42 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.16 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  1.45 (0.24), residues: 1228
  helix:  1.93 (0.20), residues: 645
  sheet:  0.30 (0.57), residues: 78
  loop : -0.15 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 997 
 TYR   0.016   0.001   TYR A 646 
 PHE   0.029   0.001   PHE A 717 
 TRP   0.008   0.001   TRP A 960 
 HIS   0.003   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10086)
  covalent geometry    : angle       0.60787 (13736)
  SS BOND              : bond        0.00243 (   13)
  SS BOND              : angle       1.02853 (   26)
  hydrogen bonds       : bond        0.05000 (  525)
  hydrogen bonds       : angle       4.71421 ( 1482)
  link_BETA1-4         : bond        0.01005 (    4)
  link_BETA1-4         : angle       3.28776 (   12)
  link_NAG-ASN         : bond        0.00257 (   14)
  link_NAG-ASN         : angle       1.71828 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7882 (mpt180) cc_final: 0.7480 (mpt180)
  outliers start: 22
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0687
  time to fit residues: 9.8047
Evaluate side-chains
  86 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  478 TYR
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  811 CYS
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue 1109 VAL
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1217 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 115 optimal weight:    9.9990
   chunk 113 optimal weight:    2.9990
   chunk 3 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 860 ASN
A1010 HIS
A1142 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.112909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.081499 restraints weight = 19155.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.080818 restraints weight = 12676.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.081255 restraints weight = 15023.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.081777 restraints weight = 9647.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.083528 restraints weight = 8193.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  10117  Z= 0.263
  Angle     :  0.758  11.540  13816  Z= 0.372
  Chirality :  0.048   0.287   1641
  Planarity :  0.005   0.037   1724
  Dihedral  :  6.555  58.078   1775
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.32 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.64 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole:  0.84 (0.24), residues: 1228
  helix:  1.51 (0.20), residues: 639
  sheet: -0.02 (0.55), residues: 78
  loop : -0.52 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 417 
 TYR   0.016   0.002   TYR A 646 
 PHE   0.017   0.002   PHE A 411 
 TRP   0.019   0.002   TRP A 960 
 HIS   0.008   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00631 (10086)
  covalent geometry    : angle       0.74185 (13736)
  SS BOND              : bond        0.00362 (   13)
  SS BOND              : angle       1.35300 (   26)
  hydrogen bonds       : bond        0.07026 (  525)
  hydrogen bonds       : angle       5.06606 ( 1482)
  link_BETA1-4         : bond        0.01025 (    4)
  link_BETA1-4         : angle       3.47410 (   12)
  link_NAG-ASN         : bond        0.00283 (   14)
  link_NAG-ASN         : angle       2.06891 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  586 MET cc_start: 0.8092 (mmm) cc_final: 0.7852 (tpp)
REVERT: A  670 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8298 (tt)
  outliers start: 27
  outliers final: 22
  residues processed: 90
  average time/residue: 0.0737
  time to fit residues: 10.3292
Evaluate side-chains
  89 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  811 CYS
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue 1109 VAL
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1217 VAL
Chi-restraints excluded: chain A residue 1253 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 111 optimal weight:    0.0870
   chunk 41 optimal weight:    0.9990
   chunk 0 optimal weight:   30.0000
   chunk 76 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A1010 HIS
A1142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.115473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.083197 restraints weight = 19136.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.083035 restraints weight = 13839.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.083636 restraints weight = 13703.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.084413 restraints weight = 9420.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.086007 restraints weight = 8224.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10117  Z= 0.121
  Angle     :  0.635  13.123  13816  Z= 0.304
  Chirality :  0.042   0.250   1641
  Planarity :  0.004   0.036   1724
  Dihedral  :  6.062  57.222   1775
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.49 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  1.30 (0.24), residues: 1228
  helix:  1.84 (0.20), residues: 643
  sheet:  0.23 (0.57), residues: 78
  loop : -0.26 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1068 
 TYR   0.015   0.001   TYR A 646 
 PHE   0.017   0.001   PHE A 717 
 TRP   0.009   0.001   TRP A 284 
 HIS   0.003   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10086)
  covalent geometry    : angle       0.62137 (13736)
  SS BOND              : bond        0.00262 (   13)
  SS BOND              : angle       0.91237 (   26)
  hydrogen bonds       : bond        0.04926 (  525)
  hydrogen bonds       : angle       4.72246 ( 1482)
  link_BETA1-4         : bond        0.01044 (    4)
  link_BETA1-4         : angle       3.25909 (   12)
  link_NAG-ASN         : bond        0.00298 (   14)
  link_NAG-ASN         : angle       1.69164 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7883 (mpt180) cc_final: 0.7411 (mpt180)
REVERT: A  586 MET cc_start: 0.7906 (mmm) cc_final: 0.7535 (mmm)
REVERT: A  788 MET cc_start: 0.8534 (mmp) cc_final: 0.8222 (mmp)
  outliers start: 19
  outliers final: 16
  residues processed: 84
  average time/residue: 0.0666
  time to fit residues: 8.8737
Evaluate side-chains
  82 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  811 CYS
Chi-restraints excluded: chain A residue 1109 VAL
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1217 VAL
Chi-restraints excluded: chain A residue 1253 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 4 optimal weight:   30.0000
   chunk 7 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 787 GLN
A1010 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.112455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.080548 restraints weight = 19274.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.079481 restraints weight = 13610.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.080546 restraints weight = 12058.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.080930 restraints weight = 9361.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.081341 restraints weight = 8744.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10117  Z= 0.217
  Angle     :  0.698  12.729  13816  Z= 0.338
  Chirality :  0.045   0.272   1641
  Planarity :  0.004   0.038   1724
  Dihedral  :  6.255  57.528   1775
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.39 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  1.04 (0.24), residues: 1228
  helix:  1.69 (0.20), residues: 639
  sheet:  0.12 (0.56), residues: 78
  loop : -0.46 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 417 
 TYR   0.017   0.002   TYR A 646 
 PHE   0.016   0.002   PHE A 411 
 TRP   0.015   0.001   TRP A 960 
 HIS   0.005   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 (10086)
  covalent geometry    : angle       0.68407 (13736)
  SS BOND              : bond        0.00313 (   13)
  SS BOND              : angle       1.07334 (   26)
  hydrogen bonds       : bond        0.06064 (  525)
  hydrogen bonds       : angle       4.88911 ( 1482)
  link_BETA1-4         : bond        0.00923 (    4)
  link_BETA1-4         : angle       3.32162 (   12)
  link_NAG-ASN         : bond        0.00228 (   14)
  link_NAG-ASN         : angle       1.86869 (   42)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7867 (mpt180) cc_final: 0.7294 (mpt180)
REVERT: A  586 MET cc_start: 0.8029 (mmm) cc_final: 0.7760 (tpp)
  outliers start: 18
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0728
  time to fit residues: 9.4217
Evaluate side-chains
  80 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   56 CYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  811 CYS
Chi-restraints excluded: chain A residue 1109 VAL
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1253 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 68 optimal weight:   20.0000
   chunk 78 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A1010 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.115152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.083690 restraints weight = 19205.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.082366 restraints weight = 13815.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.083043 restraints weight = 16258.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.083632 restraints weight = 10597.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.085044 restraints weight = 9154.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10117  Z= 0.120
  Angle     :  0.629  12.704  13816  Z= 0.300
  Chirality :  0.042   0.251   1641
  Planarity :  0.004   0.037   1724
  Dihedral  :  5.999  57.087   1775
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.39 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  1.32 (0.24), residues: 1228
  helix:  1.87 (0.21), residues: 640
  sheet:  0.30 (0.57), residues: 78
  loop : -0.28 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  63 
 TYR   0.017   0.001   TYR A 646 
 PHE   0.015   0.001   PHE A 717 
 TRP   0.008   0.001   TRP A 960 
 HIS   0.003   0.001   HIS A1054 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10086)
  covalent geometry    : angle       0.61601 (13736)
  SS BOND              : bond        0.00198 (   13)
  SS BOND              : angle       0.90419 (   26)
  hydrogen bonds       : bond        0.04875 (  525)
  hydrogen bonds       : angle       4.69862 ( 1482)
  link_BETA1-4         : bond        0.01022 (    4)
  link_BETA1-4         : angle       3.22446 (   12)
  link_NAG-ASN         : bond        0.00258 (   14)
  link_NAG-ASN         : angle       1.65037 (   42)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1390.23 seconds
wall clock time: 24 minutes 46.23 seconds (1486.23 seconds total)