Starting phenix.real_space_refine
on Tue Mar  3 23:26:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wby_21601/03_2026/6wby_21601.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wby_21601/03_2026/6wby_21601.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wby_21601/03_2026/6wby_21601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wby_21601/03_2026/6wby_21601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wby_21601/03_2026/6wby_21601.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wby_21601/03_2026/6wby_21601.cif"
  }
  resolution = 3.4
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      19      5.16       5
     C    5848      2.51       5
     N    1609      2.21       5
     O    1678      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 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: 9156
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9154
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1250, 9144
          Classifications: {'peptide': 1250}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PCIS': 1, 'PTRANS': 104, 'TRANS': 1144}
          Chain breaks: 13
          Unresolved non-hydrogen bonds: 192
          Unresolved non-hydrogen angles: 239
          Unresolved non-hydrogen dihedrals: 158
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 7, 'GLN:plan1': 1, 'TRP:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 133
      Conformer: "B"
        Number of residues, atoms: 1250, 9144
          Classifications: {'peptide': 1250}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PCIS': 1, 'PTRANS': 104, 'TRANS': 1144}
          Chain breaks: 13
          Unresolved non-hydrogen bonds: 192
          Unresolved non-hydrogen angles: 239
          Unresolved non-hydrogen dihedrals: 158
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 7, 'GLN:plan1': 1, 'TRP:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 133
          bond proxies already assigned to first conformer: 9353
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A 550 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 550 " occ=0.50
  Time building chain proxies: 3.45, per 1000 atoms: 0.38
  Number of scatterers: 9156
  At special positions: 0
  Unit cell: (128.321, 89.082, 96.5055, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      19     16.00
     O    1678      8.00
     N    1609      7.00
     C    5848      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 886 " - pdb=" SG  CYS A 895 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1104 " - pdb=" SG  CYS A1139 " 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
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 853.7 milliseconds
  

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2290

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 16 sheets defined
      33.7% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 27
      removed outlier: 3.942A  pdb=" N   ALA A  16 " --> pdb=" O   ARG A  12 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU A  23 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 45
      removed outlier: 3.501A  pdb=" N   ILE A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.602A  pdb=" N   PHE A  49 " --> pdb=" O   ASN A  45 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA A  53 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 87
    Processing helix  chain 'A' and resid 92 through 117
      removed outlier: 3.523A  pdb=" N   GLY A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ARG A 112 " --> pdb=" O   TRP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 134
      removed outlier: 3.537A  pdb=" N   ILE A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA A 131 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 140
      removed outlier: 3.820A  pdb=" N   THR A 140 " --> pdb=" O   PRO A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 148
    Processing helix  chain 'A' and resid 149 through 154
      removed outlier: 3.583A  pdb=" N   LEU A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 166
      removed outlier: 3.798A  pdb=" N   LEU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      Proline residue:  A 161  - end of helix
    Processing helix  chain 'A' and resid 171 through 185
      removed outlier: 3.740A  pdb=" N   SER A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 180 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 198
    Processing helix  chain 'A' and resid 199 through 207
      removed outlier: 3.595A  pdb=" N   TRP A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 229
      removed outlier: 3.946A  pdb=" N   TRP A 220 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      Proline residue:  A 223  - end of helix
    Processing helix  chain 'A' and resid 232 through 243
      removed outlier: 4.072A  pdb=" N   LYS A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER A 243 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 291 through 308
      removed outlier: 3.896A  pdb=" N   ALA A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR A 297 " --> pdb=" O   VAL A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 328
      removed outlier: 3.634A  pdb=" N   VAL A 319 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU A 328 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 378
      removed outlier: 3.739A  pdb=" N   ILE A 366 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A 368 " --> pdb=" O   PRO A 364 " (cutoff:3.500A)
      Proline residue:  A 369  - end of helix
      removed outlier: 3.672A  pdb=" N   LEU A 378 " --> pdb=" O   LEU A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 419
      removed outlier: 3.750A  pdb=" N   VAL A 410 " --> pdb=" O   ALA A 406 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA A 414 " --> pdb=" O   VAL A 410 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A 416 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 424
      removed outlier: 3.873A  pdb=" N   TRP A 423 " --> pdb=" O   THR A 419 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR A 424 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 419 through 424'
    Processing helix  chain 'A' and resid 437 through 448
      removed outlier: 3.682A  pdb=" N   ASN A 441 " --> pdb=" O   PRO A 437 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR A 443 " --> pdb=" O   TYR A 439 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA A 444 " --> pdb=" O   TRP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 503
      removed outlier: 3.534A  pdb=" N   ALA A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 512
      removed outlier: 3.646A  pdb=" N   PHE A 509 " --> pdb=" O   VAL A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 525
      removed outlier: 3.639A  pdb=" N   THR A 521 " --> pdb=" O   GLY A 517 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ARG A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLU A 524 " --> pdb=" O   ASP A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 554
      removed outlier: 3.547A  pdb=" N  AHIS A 550 " --> pdb=" O   PRO A 546 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   HIS A 551 " --> pdb=" O   ILE A 547 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR A 552 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 583
      No H-bonds generated for 'chain 'A' and resid 581 through 583'
    Processing helix  chain 'A' and resid 618 through 620
      No H-bonds generated for 'chain 'A' and resid 618 through 620'
    Processing helix  chain 'A' and resid 621 through 632
      removed outlier: 3.574A  pdb=" N   ARG A 630 " --> pdb=" O   ASN A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 649
      removed outlier: 3.699A  pdb=" N   ALA A 649 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 732
      removed outlier: 3.506A  pdb=" N   THR A 731 " --> pdb=" O   ALA A 728 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER A 732 " --> pdb=" O   PRO A 729 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 728 through 732'
    Processing helix  chain 'A' and resid 934 through 940
      removed outlier: 4.217A  pdb=" N   LEU A 938 " --> pdb=" O   GLN A 934 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE A 939 " --> pdb=" O   LEU A 935 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLN A 940 " --> pdb=" O   ARG A 936 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 934 through 940'
    Processing helix  chain 'A' and resid 959 through 964
      removed outlier: 3.649A  pdb=" N   ALA A 963 " --> pdb=" O   SER A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1096
      removed outlier: 3.543A  pdb=" N   ASN A1095 " --> pdb=" O   ASP A1091 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   SER A1096 " --> pdb=" O   ASN A1092 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1091 through 1096'
    Processing helix  chain 'A' and resid 1125 through 1130
      removed outlier: 3.741A  pdb=" N   ASP A1130 " --> pdb=" O   ARG A1126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1255 through 1264
      removed outlier: 3.712A  pdb=" N   GLY A1261 " --> pdb=" O   TRP A1257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1268 through 1278
    Processing helix  chain 'A' and resid 1296 through 1307
      removed outlier: 3.513A  pdb=" N   VAL A1300 " --> pdb=" O   PRO A1296 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA A1301 " --> pdb=" O   ALA A1297 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU A1303 " --> pdb=" O   GLY A1299 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A1305 " --> pdb=" O   ALA A1301 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A1307 " --> pdb=" O   LEU A1303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1336 through 1356
      removed outlier: 3.684A  pdb=" N   TYR A1341 " --> pdb=" O   ALA A1337 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER A1346 " --> pdb=" O   LEU A1342 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A1347 " --> pdb=" O   ALA A1343 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A1349 " --> pdb=" O   GLY A1345 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU A1354 " --> pdb=" O   ALA A1350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1369 through 1385
      removed outlier: 3.894A  pdb=" N   GLN A1373 " --> pdb=" O   SER A1369 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU A1374 " --> pdb=" O   TRP A1370 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER A1379 " --> pdb=" O   LEU A1375 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A1383 " --> pdb=" O   SER A1379 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58
    Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 459
      removed outlier: 6.697A  pdb=" N   ARG A 455 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   LEU A 530 " --> pdb=" O   ARG A 455 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A 457 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   VAL A 532 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL A 459 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   SER A 528 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 595 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   GLY A 566 " --> pdb=" O   PRO A 588 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL A 590 " --> pdb=" O   GLN A 564 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLN A 564 " --> pdb=" O   VAL A 590 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ILE A 592 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 579
      removed outlier: 7.041A  pdb=" N   VAL A 578 " --> pdb=" O   ARG A1061 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1181 through 1182
      removed outlier: 3.506A  pdb=" N   GLN A1236 " --> pdb=" O   VAL A1208 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   THR A1227 " --> pdb=" O   VAL A1239 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 642
      removed outlier: 7.578A  pdb=" N   ARG A 614 " --> pdb=" O   VAL A 657 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   THR A 659 " --> pdb=" O   ARG A 614 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLY A 873 " --> pdb=" O   ALA A 656 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   VAL A1163 " --> pdb=" O   ARG A 928 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ARG A 928 " --> pdb=" O   VAL A1163 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR A1169 " --> pdb=" O   THR A 922 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 708
    Processing sheet with id=AA7, first strand: chain 'A' and resid 710 through 714
      removed outlier: 6.835A  pdb=" N   THR A 817 " --> pdb=" O   LEU A 762 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLY A 794 " --> pdb=" O   THR A 791 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 746
      removed outlier: 6.797A  pdb=" N   THR A 774 " --> pdb=" O   THR A 838 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LEU A 840 " --> pdb=" O   THR A 772 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   THR A 772 " --> pdb=" O   LEU A 840 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   LEU A 842 " --> pdb=" O   ILE A 770 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ILE A 770 " --> pdb=" O   LEU A 842 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 745 through 746
      removed outlier: 4.678A  pdb=" N   LEU A 842 " --> pdb=" O   VAL A 854 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 860 through 862
      removed outlier: 4.253A  pdb=" N   ALA A 860 " --> pdb=" O   ILE A 910 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   THR A 914 " --> pdb=" O   VAL A 862 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 860 through 862
      removed outlier: 4.253A  pdb=" N   ALA A 860 " --> pdb=" O   ILE A 910 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   THR A 914 " --> pdb=" O   VAL A 862 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 886 through 887
    Processing sheet with id=AB4, first strand: chain 'A' and resid 946 through 948
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1036 through 1037
      removed outlier: 3.597A  pdb=" N   LEU A1002 " --> pdb=" O   THR A1036 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE A1078 " --> pdb=" O   ARG A1001 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1027 through 1028
      removed outlier: 3.773A  pdb=" N   ARG A1027 " --> pdb=" O   VAL A1016 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ASP A1054 " --> pdb=" O   LYS A1014 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1185 through 1186
      removed outlier: 3.522A  pdb=" N   ARG A1219 " --> pdb=" O   THR A1249 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR A1251 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    876 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: 1.83

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2824
        1.33 -     1.45: 1376
        1.45 -     1.57: 5147
        1.57 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 9377
  Sorted by residual:
  bond pdb=" CB  VAL A1229 "
       pdb=" CG2 VAL A1229 "
    ideal  model  delta    sigma   weight residual
    1.521  1.421  0.100 3.30e-02 9.18e+02 9.10e+00
  bond pdb=" CG  LEU A 559 "
       pdb=" CD2 LEU A 559 "
    ideal  model  delta    sigma   weight residual
    1.521  1.436  0.085 3.30e-02 9.18e+02 6.62e+00
  bond pdb=" CB  VAL A1239 "
       pdb=" CG2 VAL A1239 "
    ideal  model  delta    sigma   weight residual
    1.521  1.448  0.073 3.30e-02 9.18e+02 4.93e+00
  bond pdb=" C   VAL A1009 "
       pdb=" N   PRO A1010 "
    ideal  model  delta    sigma   weight residual
    1.334  1.377 -0.043 2.34e-02 1.83e+03 3.39e+00
  bond pdb=" C   ILE A  34 "
       pdb=" N   SER A  35 "
    ideal  model  delta    sigma   weight residual
    1.329  1.295  0.034 1.86e-02 2.89e+03 3.29e+00
  ... (remaining 9372 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 12465
        2.50 -     5.00: 371
        5.00 -     7.50: 45
        7.50 -     9.99: 8
        9.99 -    12.49: 3
  Bond angle restraints: 12892
  Sorted by residual:
  angle pdb=" C   ASP A  37 "
        pdb=" N   THR A  38 "
        pdb=" CA  THR A  38 "
      ideal   model   delta    sigma   weight residual
     121.54  132.02  -10.48 1.91e+00 2.74e-01 3.01e+01
  angle pdb=" N   THR A 661 "
        pdb=" CA  THR A 661 "
        pdb=" C   THR A 661 "
      ideal   model   delta    sigma   weight residual
     109.81  120.36  -10.55 2.21e+00 2.05e-01 2.28e+01
  angle pdb=" C   VAL A1117 "
        pdb=" CA  VAL A1117 "
        pdb=" CB  VAL A1117 "
      ideal   model   delta    sigma   weight residual
     111.08  115.07   -3.99 9.50e-01 1.11e+00 1.77e+01
  angle pdb=" CA  PRO A1010 "
        pdb=" N   PRO A1010 "
        pdb=" CD  PRO A1010 "
      ideal   model   delta    sigma   weight residual
     112.00  106.79    5.21 1.40e+00 5.10e-01 1.39e+01
  angle pdb=" CA  VAL A1009 "
        pdb=" C   VAL A1009 "
        pdb=" N   PRO A1010 "
      ideal   model   delta    sigma   weight residual
     118.88  124.45   -5.57 1.54e+00 4.22e-01 1.31e+01
  ... (remaining 12887 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 5111
       17.82 -    35.64: 377
       35.64 -    53.47: 51
       53.47 -    71.29: 4
       71.29 -    89.11: 5
  Dihedral angle restraints: 5548
    sinusoidal: 2007
      harmonic: 3541
  Sorted by residual:
  dihedral pdb=" CA  GLU A1008 "
           pdb=" C   GLU A1008 "
           pdb=" N   VAL A1009 "
           pdb=" CA  VAL A1009 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.26  -28.74     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  PRO A 866 "
           pdb=" C   PRO A 866 "
           pdb=" N   ALA A 867 "
           pdb=" CA  ALA A 867 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.12  -27.88     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" CA  PRO A1010 "
           pdb=" C   PRO A1010 "
           pdb=" N   ALA A1011 "
           pdb=" CA  ALA A1011 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.41  -26.59     0      5.00e+00 4.00e-02 2.83e+01
  ... (remaining 5545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1451
       0.118 -    0.235: 89
       0.235 -    0.353: 5
       0.353 -    0.470: 0
       0.470 -    0.588: 1
  Chirality restraints: 1546
  Sorted by residual:
  chirality pdb=" CB  ILE A 145 "
            pdb=" CA  ILE A 145 "
            pdb=" CG1 ILE A 145 "
            pdb=" CG2 ILE A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.06    0.59 2.00e-01 2.50e+01 8.64e+00
  chirality pdb=" CA  THR A 661 "
            pdb=" N   THR A 661 "
            pdb=" C   THR A 661 "
            pdb=" CB  THR A 661 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.18    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CB  ILE A 491 "
            pdb=" CA  ILE A 491 "
            pdb=" CG1 ILE A 491 "
            pdb=" CG2 ILE A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 1543 not shown)

  Planarity restraints: 1661
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 155 "   -0.048 5.00e-02 4.00e+02   7.12e-02 8.11e+00
        pdb=" N   PRO A 156 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 156 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 156 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 974 "    0.047 5.00e-02 4.00e+02   7.12e-02 8.11e+00
        pdb=" N   PRO A 975 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 975 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 975 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A  37 "   -0.014 2.00e-02 2.50e+03   2.81e-02 7.90e+00
        pdb=" C   ASP A  37 "    0.049 2.00e-02 2.50e+03
        pdb=" O   ASP A  37 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR A  38 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1658 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 94
        2.61 -     3.19: 7338
        3.19 -     3.76: 13386
        3.76 -     4.33: 18552
        4.33 -     4.90: 32385
  Nonbonded interactions: 71755
  Sorted by model distance:
  nonbonded pdb=" O   THR A 838 "
            pdb=" OE2 GLU A 839 "
     model   vdw
     2.042 3.040
  nonbonded pdb=" O   ALA A 962 "
            pdb="CA    CA A2002 "
     model   vdw
     2.067 2.510
  nonbonded pdb=" OG  SER A 715 "
            pdb=" OE1 GLN A 756 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASP A 967 "
            pdb="CA    CA A2002 "
     model   vdw
     2.263 2.510
  nonbonded pdb=" O   THR A 970 "
            pdb="CA    CA A2002 "
     model   vdw
     2.296 2.510
  ... (remaining 71750 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.390
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
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      :  0.010   0.100   9379  Z= 0.422
  Angle     :  1.037  12.493  12896  Z= 0.579
  Chirality :  0.063   0.588   1546
  Planarity :  0.009   0.071   1661
  Dihedral  : 12.683  89.109   3252
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.30 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  6.13 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -5.12 (0.18), residues: 1225
  helix: -4.98 (0.08), residues: 382
  sheet: -2.14 (0.32), residues: 197
  loop : -2.77 (0.20), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 687 
 TYR   0.014   0.002   TYR A1258 
 PHE   0.025   0.003   PHE A 433 
 TRP   0.028   0.003   TRP A 221 
 HIS   0.014   0.002   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.01006 ( 9377)
  covalent geometry    : angle       1.03707 (12892)
  SS BOND              : bond        0.00497 (    2)
  SS BOND              : angle       0.65389 (    4)
  hydrogen bonds       : bond        0.30186 (  303)
  hydrogen bonds       : angle      11.29681 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 MET cc_start: 0.8288 (mtt) cc_final: 0.8074 (mtt)
REVERT: A  739 ARG cc_start: 0.7207 (mpt-90) cc_final: 0.6968 (mpt180)
REVERT: A 1034 ASP cc_start: 0.7167 (m-30) cc_final: 0.6960 (m-30)
  outliers start: 3
  outliers final: 2
  residues processed: 88
  average time/residue: 0.1215
  time to fit residues: 14.2345
Evaluate side-chains
  63 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  830 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 123 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 551 HIS
A1151 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.152230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.125441 restraints weight = 24914.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 3.03
r_work: 0.3307 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9379  Z= 0.128
  Angle     :  0.623   8.686  12896  Z= 0.311
  Chirality :  0.044   0.406   1546
  Planarity :  0.006   0.056   1661
  Dihedral  :  5.291  33.182   1322
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.28 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -3.56 (0.20), residues: 1225
  helix: -3.17 (0.19), residues: 376
  sheet: -1.55 (0.34), residues: 197
  loop : -2.08 (0.22), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1192 
 TYR   0.012   0.002   TYR A 845 
 PHE   0.014   0.001   PHE A 246 
 TRP   0.015   0.001   TRP A 214 
 HIS   0.003   0.001   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9377)
  covalent geometry    : angle       0.62343 (12892)
  SS BOND              : bond        0.00085 (    2)
  SS BOND              : angle       0.21304 (    4)
  hydrogen bonds       : bond        0.04796 (  303)
  hydrogen bonds       : angle       6.13043 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  309 MET cc_start: 0.8242 (mtt) cc_final: 0.8019 (mtt)
REVERT: A  739 ARG cc_start: 0.7986 (mpt-90) cc_final: 0.7729 (mpt180)
REVERT: A 1034 ASP cc_start: 0.7292 (m-30) cc_final: 0.6976 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0924
  time to fit residues: 11.1786
Evaluate side-chains
  67 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  713 THR
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue 1015 GLN
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain A residue 1152 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 114 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0020
   chunk 121 optimal weight:    5.9990
   overall best weight:    1.2592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.145882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.121019 restraints weight = 23647.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.73
r_work: 0.3313 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9379  Z= 0.175
  Angle     :  0.629   9.393  12896  Z= 0.307
  Chirality :  0.046   0.435   1546
  Planarity :  0.005   0.054   1661
  Dihedral  :  4.980  35.879   1322
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.32 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -2.70 (0.22), residues: 1225
  helix: -2.01 (0.24), residues: 382
  sheet: -1.24 (0.35), residues: 198
  loop : -1.79 (0.23), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1106 
 TYR   0.014   0.001   TYR A 439 
 PHE   0.022   0.001   PHE A 246 
 TRP   0.013   0.001   TRP A 214 
 HIS   0.005   0.001   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 9377)
  covalent geometry    : angle       0.62903 (12892)
  SS BOND              : bond        0.00145 (    2)
  SS BOND              : angle       0.32029 (    4)
  hydrogen bonds       : bond        0.04170 (  303)
  hydrogen bonds       : angle       5.38176 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  739 ARG cc_start: 0.8188 (mpt-90) cc_final: 0.7906 (mpt180)
  outliers start: 13
  outliers final: 11
  residues processed: 73
  average time/residue: 0.0940
  time to fit residues: 9.7602
Evaluate side-chains
  71 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  713 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue 1015 GLN
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1152 ASP
Chi-restraints excluded: chain A residue 1336 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 35 optimal weight:    0.0050
   chunk 45 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 124 optimal weight:    9.9990
   chunk 87 optimal weight:    9.9990
   chunk 110 optimal weight:    0.7980
   chunk 114 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.5794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.149320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.125548 restraints weight = 32702.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 4.27
r_work: 0.3308 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9379  Z= 0.109
  Angle     :  0.566   8.655  12896  Z= 0.275
  Chirality :  0.044   0.507   1546
  Planarity :  0.005   0.049   1661
  Dihedral  :  4.594  35.175   1322
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.54 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -2.02 (0.23), residues: 1225
  helix: -1.21 (0.26), residues: 376
  sheet: -0.92 (0.36), residues: 198
  loop : -1.52 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1106 
 TYR   0.010   0.001   TYR A 439 
 PHE   0.008   0.001   PHE A1066 
 TRP   0.011   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9377)
  covalent geometry    : angle       0.56650 (12892)
  SS BOND              : bond        0.00063 (    2)
  SS BOND              : angle       0.26449 (    4)
  hydrogen bonds       : bond        0.03257 (  303)
  hydrogen bonds       : angle       4.89567 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7822 (mt-10)
REVERT: A  739 ARG cc_start: 0.8107 (mpt-90) cc_final: 0.7904 (mpt180)
  outliers start: 15
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0928
  time to fit residues: 10.6198
Evaluate side-chains
  70 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  988 VAL
Chi-restraints excluded: chain A residue 1015 GLN
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain A residue 1152 ASP
Chi-restraints excluded: chain A residue 1336 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 87 optimal weight:    9.9990
   chunk 93 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0970
   chunk 119 optimal weight:    4.9990
   overall best weight:    0.6178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.149138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.124331 restraints weight = 22645.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.66
r_work: 0.3367 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9379  Z= 0.112
  Angle     :  0.559   8.612  12896  Z= 0.271
  Chirality :  0.045   0.528   1546
  Planarity :  0.005   0.046   1661
  Dihedral  :  4.424  35.127   1322
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.61 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -1.61 (0.23), residues: 1225
  helix: -0.73 (0.27), residues: 379
  sheet: -0.69 (0.37), residues: 196
  loop : -1.37 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 523 
 TYR   0.017   0.001   TYR A  71 
 PHE   0.008   0.001   PHE A 433 
 TRP   0.011   0.001   TRP A 214 
 HIS   0.003   0.001   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9377)
  covalent geometry    : angle       0.55904 (12892)
  SS BOND              : bond        0.00067 (    2)
  SS BOND              : angle       0.26280 (    4)
  hydrogen bonds       : bond        0.03110 (  303)
  hydrogen bonds       : angle       4.66495 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.8213 (mt-10) cc_final: 0.8005 (mt-10)
  outliers start: 14
  outliers final: 13
  residues processed: 76
  average time/residue: 0.0886
  time to fit residues: 9.7671
Evaluate side-chains
  76 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  988 VAL
Chi-restraints excluded: chain A residue 1015 GLN
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1152 ASP
Chi-restraints excluded: chain A residue 1336 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 120 optimal weight:    8.9990
   chunk 96 optimal weight:    3.9990
   chunk 123 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    1.0382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.151503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.125682 restraints weight = 26958.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 3.11
r_work: 0.3308 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9379  Z= 0.147
  Angle     :  0.575   8.693  12896  Z= 0.279
  Chirality :  0.046   0.550   1546
  Planarity :  0.005   0.046   1661
  Dihedral  :  4.486  35.850   1322
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.40 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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 (0.24), residues: 1225
  helix: -0.44 (0.27), residues: 380
  sheet: -0.65 (0.36), residues: 196
  loop : -1.33 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 523 
 TYR   0.014   0.002   TYR A  71 
 PHE   0.011   0.001   PHE A 433 
 TRP   0.011   0.001   TRP A 214 
 HIS   0.004   0.001   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9377)
  covalent geometry    : angle       0.57460 (12892)
  SS BOND              : bond        0.00116 (    2)
  SS BOND              : angle       0.35529 (    4)
  hydrogen bonds       : bond        0.03268 (  303)
  hydrogen bonds       : angle       4.62417 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7918 (mt-10)
REVERT: A  312 MET cc_start: 0.8279 (ttt) cc_final: 0.7970 (tpt)
  outliers start: 18
  outliers final: 18
  residues processed: 76
  average time/residue: 0.0867
  time to fit residues: 9.6335
Evaluate side-chains
  78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  713 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  841 SER
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  988 VAL
Chi-restraints excluded: chain A residue 1007 THR
Chi-restraints excluded: chain A residue 1015 GLN
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1206 LEU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1336 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 120 optimal weight:    8.9990
   chunk 103 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 99 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0270
   chunk 40 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5438

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.149949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.125445 restraints weight = 29996.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 3.49
r_work: 0.3339 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3345
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3345
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9379  Z= 0.105
  Angle     :  0.546   8.274  12896  Z= 0.265
  Chirality :  0.045   0.561   1546
  Planarity :  0.004   0.045   1661
  Dihedral  :  4.311  35.234   1322
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.15 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -1.14 (0.24), residues: 1225
  helix: -0.10 (0.28), residues: 379
  sheet: -0.50 (0.37), residues: 197
  loop : -1.20 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 523 
 TYR   0.015   0.001   TYR A  71 
 PHE   0.007   0.001   PHE A 433 
 TRP   0.010   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9377)
  covalent geometry    : angle       0.54578 (12892)
  SS BOND              : bond        0.00041 (    2)
  SS BOND              : angle       0.26249 (    4)
  hydrogen bonds       : bond        0.02938 (  303)
  hydrogen bonds       : angle       4.45447 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7857 (mt-10)
REVERT: A  312 MET cc_start: 0.8251 (ttt) cc_final: 0.7987 (tpt)
  outliers start: 18
  outliers final: 15
  residues processed: 79
  average time/residue: 0.0964
  time to fit residues: 10.8267
Evaluate side-chains
  80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  713 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  841 SER
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  988 VAL
Chi-restraints excluded: chain A residue 1015 GLN
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1152 ASP
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1336 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0770
   chunk 26 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0770
   overall best weight:    0.5296

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.150518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.125521 restraints weight = 23460.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.67
r_work: 0.3394 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3258
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3258
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9379  Z= 0.104
  Angle     :  0.538   8.253  12896  Z= 0.260
  Chirality :  0.045   0.581   1546
  Planarity :  0.004   0.044   1661
  Dihedral  :  4.171  34.992   1322
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.01 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.93 (0.24), residues: 1225
  helix:  0.17 (0.28), residues: 380
  sheet: -0.37 (0.37), residues: 196
  loop : -1.15 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 523 
 TYR   0.017   0.001   TYR A  71 
 PHE   0.010   0.001   PHE A1066 
 TRP   0.010   0.001   TRP A 214 
 HIS   0.002   0.001   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9377)
  covalent geometry    : angle       0.53849 (12892)
  SS BOND              : bond        0.00055 (    2)
  SS BOND              : angle       0.26597 (    4)
  hydrogen bonds       : bond        0.02838 (  303)
  hydrogen bonds       : angle       4.32997 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  312 MET cc_start: 0.8302 (ttt) cc_final: 0.8012 (tpt)
  outliers start: 15
  outliers final: 14
  residues processed: 78
  average time/residue: 0.0986
  time to fit residues: 10.8708
Evaluate side-chains
  78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  713 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  841 SER
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  988 VAL
Chi-restraints excluded: chain A residue 1015 GLN
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1336 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 115 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 123 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0770
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.6538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.150210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.125086 restraints weight = 27035.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 3.09
r_work: 0.3352 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9379  Z= 0.112
  Angle     :  0.542   8.288  12896  Z= 0.262
  Chirality :  0.045   0.593   1546
  Planarity :  0.004   0.045   1661
  Dihedral  :  4.154  35.285   1322
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.12 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.74 (0.24), residues: 1225
  helix:  0.39 (0.28), residues: 377
  sheet: -0.28 (0.37), residues: 196
  loop : -1.07 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 523 
 TYR   0.017   0.001   TYR A  71 
 PHE   0.008   0.001   PHE A 433 
 TRP   0.013   0.001   TRP A 423 
 HIS   0.003   0.001   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9377)
  covalent geometry    : angle       0.54179 (12892)
  SS BOND              : bond        0.00063 (    2)
  SS BOND              : angle       0.25836 (    4)
  hydrogen bonds       : bond        0.02884 (  303)
  hydrogen bonds       : angle       4.28666 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  312 MET cc_start: 0.8199 (ttt) cc_final: 0.7916 (tpt)
  outliers start: 18
  outliers final: 17
  residues processed: 76
  average time/residue: 0.0982
  time to fit residues: 10.6469
Evaluate side-chains
  77 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  713 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  841 SER
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  988 VAL
Chi-restraints excluded: chain A residue 1015 GLN
Chi-restraints excluded: chain A residue 1035 VAL
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1152 ASP
Chi-restraints excluded: chain A residue 1206 LEU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1336 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 25 optimal weight:    9.9990
   chunk 117 optimal weight:    0.0870
   chunk 29 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.3362

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.150687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.124624 restraints weight = 25953.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 3.07
r_work: 0.3296 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3308
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3308
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9379  Z= 0.177
  Angle     :  0.587   8.791  12896  Z= 0.285
  Chirality :  0.047   0.592   1546
  Planarity :  0.005   0.045   1661
  Dihedral  :  4.413  36.338   1322
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.23 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.81 (0.24), residues: 1225
  helix:  0.37 (0.28), residues: 377
  sheet: -0.40 (0.37), residues: 197
  loop : -1.10 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.017   0.002   TYR A  71 
 PHE   0.012   0.001   PHE A 433 
 TRP   0.012   0.001   TRP A 423 
 HIS   0.004   0.001   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 9377)
  covalent geometry    : angle       0.58660 (12892)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       0.38404 (    4)
  hydrogen bonds       : bond        0.03298 (  303)
  hydrogen bonds       : angle       4.45398 (  876)

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  312 MET cc_start: 0.8297 (ttt) cc_final: 0.8008 (tpt)
  outliers start: 17
  outliers final: 17
  residues processed: 69
  average time/residue: 0.0997
  time to fit residues: 9.8877
Evaluate side-chains
  74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  713 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  841 SER
Chi-restraints excluded: chain A residue  913 LEU
Chi-restraints excluded: chain A residue  988 VAL
Chi-restraints excluded: chain A residue 1015 GLN
Chi-restraints excluded: chain A residue 1035 VAL
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1206 LEU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1336 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0270
   chunk 58 optimal weight:    0.2980
   chunk 15 optimal weight:    0.2980
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.5038

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.150227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.125211 restraints weight = 24435.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 2.75
r_work: 0.3370 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3383
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3383
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9379  Z= 0.102
  Angle     :  0.540   8.235  12896  Z= 0.262
  Chirality :  0.045   0.601   1546
  Planarity :  0.004   0.043   1661
  Dihedral  :  4.200  35.347   1322
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.12 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.63 (0.24), residues: 1225
  helix:  0.56 (0.28), residues: 378
  sheet: -0.26 (0.37), residues: 196
  loop : -1.04 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 523 
 TYR   0.019   0.001   TYR A  71 
 PHE   0.007   0.001   PHE A  75 
 TRP   0.010   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9377)
  covalent geometry    : angle       0.54052 (12892)
  SS BOND              : bond        0.00032 (    2)
  SS BOND              : angle       0.26018 (    4)
  hydrogen bonds       : bond        0.02840 (  303)
  hydrogen bonds       : angle       4.28615 (  876)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2042.20 seconds
wall clock time: 35 minutes 33.80 seconds (2133.80 seconds total)