Starting phenix.real_space_refine
on Fri May 16 05:48:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eqv_28547/05_2025/8eqv_28547.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eqv_28547/05_2025/8eqv_28547.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eqv_28547/05_2025/8eqv_28547.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eqv_28547/05_2025/8eqv_28547.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eqv_28547/05_2025/8eqv_28547.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eqv_28547/05_2025/8eqv_28547.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      97      5.16       5
     C    8839      2.51       5
     N    2459      2.21       5
     O    2579      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13974
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 3117
          Classifications: {'peptide': 391}
          Link IDs: {'PTRANS': 22, 'TRANS': 368}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 870
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 2902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2902
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 12, 'TRANS': 349}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "D"
      Number of atoms: 3519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 466, 3519
          Classifications: {'peptide': 466}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 22, 'TRANS': 443}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 248
          Unresolved non-hydrogen angles: 304
          Unresolved non-hydrogen dihedrals: 212
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 159
    Chain: "B"
      Number of atoms: 3566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3566
          Classifications: {'peptide': 438}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 19, 'TRANS': 418}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 44
  Time building chain proxies: 8.49, per 1000 atoms: 0.61
  Number of scatterers: 13974
  At special positions: 0
  Unit cell: (92.88, 109.22, 170.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      97     16.00
     O    2579      8.00
     N    2459      7.00
     C    8839      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 409 " - pdb=" SG  CYS E 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 289 " - pdb=" SG  CYS D 294 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 523 " - pdb=" SG  CYS D 547 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 523 " - pdb=" SG  CYS D 549 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 549 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 553 " distance=2.04

  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: 3.08
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3382

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 23 sheets defined
      23.3% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 27
    Processing helix  chain 'A' and resid 28 through 30
      No H-bonds generated for 'chain 'A' and resid 28 through 30'
    Processing helix  chain 'A' and resid 355 through 362
      removed outlier: 3.628A  pdb=" N   GLY A 362 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.330A  pdb=" N   TYR A 409 " --> pdb=" O   ALA A 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 418
      removed outlier: 3.518A  pdb=" N   HIS C 418 " --> pdb=" O   ASN C 414 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 465 through 468
      removed outlier: 3.728A  pdb=" N   HIS C 468 " --> pdb=" O   SER C 465 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 465 through 468'
    Processing helix  chain 'C' and resid 478 through 480
      No H-bonds generated for 'chain 'C' and resid 478 through 480'
    Processing helix  chain 'C' and resid 481 through 486
      removed outlier: 4.200A  pdb=" N   LEU C 486 " --> pdb=" O   LYS C 482 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 128 through 130
      No H-bonds generated for 'chain 'E' and resid 128 through 130'
    Processing helix  chain 'E' and resid 267 through 278
    Processing helix  chain 'E' and resid 281 through 285
      removed outlier: 3.919A  pdb=" N   THR E 285 " --> pdb=" O   PRO E 282 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 15 through 19
    Processing helix  chain 'D' and resid 23 through 61
      removed outlier: 3.623A  pdb=" N   GLU D  51 " --> pdb=" O   GLN D  47 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ARG D  52 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 181
    Processing helix  chain 'D' and resid 219 through 223
    Processing helix  chain 'D' and resid 224 through 229
      removed outlier: 3.578A  pdb=" N   SER D 229 " --> pdb=" O   GLU D 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 238 through 247
    Processing helix  chain 'D' and resid 274 through 283
      removed outlier: 3.602A  pdb=" N   LEU D 278 " --> pdb=" O   ARG D 274 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 328 through 340
    Processing helix  chain 'D' and resid 435 through 448
      removed outlier: 3.787A  pdb=" N   MET D 439 " --> pdb=" O   ALA D 435 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 452 through 458
    Processing helix  chain 'D' and resid 462 through 475
    Processing helix  chain 'D' and resid 571 through 576
      removed outlier: 3.860A  pdb=" N   ALA D 576 " --> pdb=" O   PRO D 572 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 604 through 609
      removed outlier: 4.276A  pdb=" N   ARG D 608 " --> pdb=" O   CYS D 604 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 647 through 659
    Processing helix  chain 'D' and resid 682 through 686
      removed outlier: 3.796A  pdb=" N   PHE D 686 " --> pdb=" O   LYS D 683 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 90
    Processing helix  chain 'B' and resid 90 through 107
      removed outlier: 3.990A  pdb=" N   GLN B  95 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE B  96 " --> pdb=" O   LYS B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 122
      removed outlier: 3.575A  pdb=" N   LEU B 115 " --> pdb=" O   HIS B 112 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   THR B 116 " --> pdb=" O   ARG B 113 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   TYR B 117 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   MET B 118 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER B 119 " --> pdb=" O   THR B 116 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   HIS B 120 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 147
      removed outlier: 3.669A  pdb=" N   MET B 137 " --> pdb=" O   LYS B 133 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU B 138 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU B 147 " --> pdb=" O   LYS B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 471
      removed outlier: 3.512A  pdb=" N   HIS B 471 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 601
    Processing helix  chain 'B' and resid 607 through 625
      removed outlier: 4.613A  pdb=" N   VAL B 613 " --> pdb=" O   GLY B 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 643
      removed outlier: 4.601A  pdb=" N   HIS B 634 " --> pdb=" O   ASN B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 643 through 651
    Processing helix  chain 'B' and resid 652 through 666
    Processing helix  chain 'B' and resid 670 through 685
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 39
      removed outlier: 3.522A  pdb=" N   LEU A  34 " --> pdb=" O   GLN A 403 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ILE A 398 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ASP A 379 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49
      removed outlier: 4.109A  pdb=" N   ASN A  77 " --> pdb=" O   HIS A 123 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ILE A 121 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   SER A  83 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   ILE A 117 " --> pdb=" O   SER A  83 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   GLN A  85 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE A 115 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 132
      removed outlier: 3.613A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA A 141 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE A 140 " --> pdb=" O   PHE A 152 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL A 151 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 184
      removed outlier: 3.677A  pdb=" N   GLY A 182 " --> pdb=" O   ALA A 196 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   THR A 221 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 235
      removed outlier: 4.135A  pdb=" N   PHE A 243 " --> pdb=" O   TRP A 255 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA A 247 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   LYS A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   HIS A 267 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 281
      removed outlier: 6.734A  pdb=" N   GLY A 292 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LEU A 279 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA A 290 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   PHE A 281 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   ILE A 288 " --> pdb=" O   PHE A 281 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A 289 " --> pdb=" O   TRP A 301 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   THR A 291 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 325
      removed outlier: 3.547A  pdb=" N   GLN A 322 " --> pdb=" O   SER A 336 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 427 through 431
    Processing sheet with id=AA9, first strand: chain 'C' and resid 461 through 463
      removed outlier: 4.450A  pdb=" N   ALA C 436 " --> pdb=" O   LEU C 448 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   ILE C 435 " --> pdb=" O   ALA B 318 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA B 318 " --> pdb=" O   ILE C 435 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   THR B 354 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   PHE B 164 " --> pdb=" O   THR B 354 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   GLN B 356 " --> pdb=" O   THR B 162 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 413 through 418
      removed outlier: 4.745A  pdb=" N   GLN E 415 " --> pdb=" O   VAL E 428 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL E 428 " --> pdb=" O   GLN E 415 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ALA E 427 " --> pdb=" O   TRP E 435 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER E 433 " --> pdb=" O   CYS E 429 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG E 436 " --> pdb=" O   ASN E  86 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   ASN E  86 " --> pdb=" O   ARG E 436 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP E 438 " --> pdb=" O   CYS E  84 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   CYS E  84 " --> pdb=" O   ASP E 438 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS E  89 " --> pdb=" O   THR D  86 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 98 through 101
      removed outlier: 3.728A  pdb=" N   GLY E  98 " --> pdb=" O   VAL E 116 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL E 116 " --> pdb=" O   GLY E  98 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL E 121 " --> pdb=" O   SER E 137 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   SER E 137 " --> pdb=" O   VAL E 121 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   LEU E 123 " --> pdb=" O   LEU E 135 " (cutoff:3.500A)
      removed outlier: 8.941A  pdb=" N   LYS D  99 " --> pdb=" O   LEU E 135 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER E 137 " --> pdb=" O   LYS D  99 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 154
      removed outlier: 7.090A  pdb=" N   ALA E 166 " --> pdb=" O   TYR E 148 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   CYS E 150 " --> pdb=" O   ALA E 164 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ALA E 164 " --> pdb=" O   CYS E 150 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   TRP E 152 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU E 162 " --> pdb=" O   TRP E 152 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLY E 167 " --> pdb=" O   ILE E 171 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   ILE E 171 " --> pdb=" O   GLY E 167 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ASN E 176 " --> pdb=" O   CYS E 182 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   CYS E 182 " --> pdb=" O   ASN E 176 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 193 through 198
      removed outlier: 3.677A  pdb=" N   GLU E 195 " --> pdb=" O   VAL E 209 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   LEU E 215 " --> pdb=" O   ILE E 228 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ILE E 228 " --> pdb=" O   LEU E 215 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   LEU E 217 " --> pdb=" O   VAL E 226 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 239 through 244
      removed outlier: 3.830A  pdb=" N   PHE E 299 " --> pdb=" O   LEU E 262 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 309 through 315
      removed outlier: 4.577A  pdb=" N   CYS E 311 " --> pdb=" O   LYS E 322 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   SER E 323 " --> pdb=" O   ALA E 327 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   ALA E 327 " --> pdb=" O   SER E 323 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   LYS E 332 " --> pdb=" O   ILE E 352 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ILE E 352 " --> pdb=" O   LYS E 332 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 370
    Processing sheet with id=AB8, first strand: chain 'D' and resid 114 through 115
      removed outlier: 5.872A  pdb=" N   SER D 114 " --> pdb=" O   GLY D 681 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 121
      removed outlier: 6.474A  pdb=" N   PHE D 120 " --> pdb=" O   ILE D 645 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 614 through 618
    Processing sheet with id=AC2, first strand: chain 'D' and resid 637 through 640
      removed outlier: 7.004A  pdb=" N   PHE D 637 " --> pdb=" O   ALA D 712 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ALA D 712 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER D 639 " --> pdb=" O   ILE D 710 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 207
      removed outlier: 6.736A  pdb=" N   VAL B 191 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 207
      removed outlier: 3.670A  pdb=" N   LEU B 187 " --> pdb=" O   LEU B 251 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 437 through 441
      removed outlier: 7.150A  pdb=" N   PHE B 432 " --> pdb=" O   ARG B 439 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   GLN B 441 " --> pdb=" O   TYR B 430 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   TYR B 430 " --> pdb=" O   GLN B 441 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B 489 " --> pdb=" O   GLN B 431 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG B 486 " --> pdb=" O   VAL B 479 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL B 479 " --> pdb=" O   ARG B 486 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN B 477 " --> pdb=" O   ASP B 488 " (cutoff:3.500A)

    447 hydrogen bonds defined for protein.
    1260 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: 4.20

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4617
        1.35 -     1.47: 3402
        1.47 -     1.59: 6151
        1.59 -     1.71: 0
        1.71 -     1.83: 136
  Bond restraints: 14306
  Sorted by residual:
  bond pdb=" CA  ASP E 212 "
       pdb=" C   ASP E 212 "
    ideal  model  delta    sigma   weight residual
    1.523  1.495  0.029 1.56e-02 4.11e+03 3.37e+00
  bond pdb=" C   LYS A 143 "
       pdb=" N   THR A 144 "
    ideal  model  delta    sigma   weight residual
    1.330  1.304  0.026 1.47e-02 4.63e+03 3.24e+00
  bond pdb=" C   MET C 452 "
       pdb=" N   PRO C 453 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.023 1.36e-02 5.41e+03 2.89e+00
  bond pdb=" CA  ASN B 216 "
       pdb=" CB  ASN B 216 "
    ideal  model  delta    sigma   weight residual
    1.522  1.531 -0.009 7.00e-03 2.04e+04 1.53e+00
  bond pdb=" CA  ASP E 395 "
       pdb=" C   ASP E 395 "
    ideal  model  delta    sigma   weight residual
    1.524  1.539 -0.015 1.26e-02 6.30e+03 1.49e+00
  ... (remaining 14301 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 19148
        2.82 -     5.65: 214
        5.65 -     8.47: 13
        8.47 -    11.29: 2
       11.29 -    14.11: 1
  Bond angle restraints: 19378
  Sorted by residual:
  angle pdb=" C   LYS A 143 "
        pdb=" N   THR A 144 "
        pdb=" CA  THR A 144 "
      ideal   model   delta    sigma   weight residual
     120.68  134.79  -14.11 1.52e+00 4.33e-01 8.62e+01
  angle pdb=" C   ARG B 253 "
        pdb=" N   VAL B 254 "
        pdb=" CA  VAL B 254 "
      ideal   model   delta    sigma   weight residual
     121.97  131.15   -9.18 1.80e+00 3.09e-01 2.60e+01
  angle pdb=" C   LYS B 537 "
        pdb=" CA  LYS B 537 "
        pdb=" CB  LYS B 537 "
      ideal   model   delta    sigma   weight residual
     115.79  110.16    5.63 1.19e+00 7.06e-01 2.23e+01
  angle pdb=" N   VAL D 691 "
        pdb=" CA  VAL D 691 "
        pdb=" C   VAL D 691 "
      ideal   model   delta    sigma   weight residual
     111.90  108.70    3.20 8.10e-01 1.52e+00 1.57e+01
  angle pdb=" N   ILE D 538 "
        pdb=" CA  ILE D 538 "
        pdb=" C   ILE D 538 "
      ideal   model   delta    sigma   weight residual
     112.80  108.52    4.28 1.15e+00 7.56e-01 1.38e+01
  ... (remaining 19373 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 7437
       17.81 -    35.61: 912
       35.61 -    53.42: 197
       53.42 -    71.23: 30
       71.23 -    89.03: 16
  Dihedral angle restraints: 8592
    sinusoidal: 3418
      harmonic: 5174
  Sorted by residual:
  dihedral pdb=" CB  CYS D 523 "
           pdb=" SG  CYS D 523 "
           pdb=" SG  CYS D 549 "
           pdb=" CB  CYS D 549 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.69   58.69     1      1.00e+01 1.00e-02 4.61e+01
  dihedral pdb=" CA  ASP D 531 "
           pdb=" C   ASP D 531 "
           pdb=" N   SER D 532 "
           pdb=" CA  SER D 532 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.49  -28.51     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  CYS D 294 "
           pdb=" C   CYS D 294 "
           pdb=" N   PHE D 295 "
           pdb=" CA  PHE D 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.46  -24.54     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 8589 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1443
       0.037 -    0.074: 472
       0.074 -    0.111: 164
       0.111 -    0.148: 39
       0.148 -    0.185: 3
  Chirality restraints: 2121
  Sorted by residual:
  chirality pdb=" CA  ASP E 395 "
            pdb=" N   ASP E 395 "
            pdb=" C   ASP E 395 "
            pdb=" CB  ASP E 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.52e-01
  chirality pdb=" CA  GLU C 454 "
            pdb=" N   GLU C 454 "
            pdb=" C   GLU C 454 "
            pdb=" CB  GLU C 454 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.06e-01
  chirality pdb=" CB  ILE A 369 "
            pdb=" CA  ILE A 369 "
            pdb=" CG1 ILE A 369 "
            pdb=" CG2 ILE A 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.46e-01
  ... (remaining 2118 not shown)

  Planarity restraints: 2499
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  96 "    0.048 5.00e-02 4.00e+02   7.40e-02 8.75e+00
        pdb=" N   PRO D  97 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO D  97 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO D  97 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  32 "   -0.015 2.00e-02 2.50e+03   1.60e-02 4.50e+00
        pdb=" CG  PHE D  32 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  32 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  32 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  32 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  32 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  32 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 253 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.38e+00
        pdb=" C   ARG B 253 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ARG B 253 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL B 254 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2496 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 947
        2.73 -     3.27: 13920
        3.27 -     3.82: 22540
        3.82 -     4.36: 26390
        4.36 -     4.90: 45043
  Nonbonded interactions: 108840
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 676 "
            pdb=" OG1 THR D 678 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" O   LEU B 311 "
            pdb=" OH  TYR B 315 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OH  TYR A 284 "
            pdb=" O   PRO A 327 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OE2 GLU A  13 "
            pdb=" NH2 ARG B 103 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" O   HIS D 593 "
            pdb=" NH2 ARG D 608 "
     model   vdw
     2.235 3.120
  ... (remaining 108835 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=0.06 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.240
  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:             0.010
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.110
  Set scattering table:                    0.120
  Process input model:                     31.740
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
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      :  0.003   0.039  14312  Z= 0.171
  Angle     :  0.783  14.114  19390  Z= 0.472
  Chirality :  0.043   0.185   2121
  Planarity :  0.005   0.074   2499
  Dihedral  : 16.230  89.034   5192
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.26 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 21.16 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.20), residues: 1719
  helix:  0.89 (0.29), residues: 343
  sheet: -1.38 (0.26), residues: 393
  loop : -2.17 (0.19), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 361 
 HIS   0.010   0.001   HIS B 449 
 PHE   0.037   0.002   PHE D  32 
 TYR   0.016   0.001   TYR A 284 
 ARG   0.007   0.001   ARG D 685 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17741 (  443)
  hydrogen bonds       : angle       7.01211 ( 1260)
  SS BOND              : bond        0.00681 (    6)
  SS BOND              : angle       1.77627 (   12)
  covalent geometry    : bond        0.00321 (14306)
  covalent geometry    : angle       0.78200 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 1.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  439 MET cc_start: 0.9145 (ttp) cc_final: 0.8674 (tmm)
REVERT: B  299 MET cc_start: 0.9488 (ttm) cc_final: 0.8982 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 106
  average time/residue: 0.3188
  time to fit residues: 50.4486
Evaluate side-chains
  72 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 1.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  261 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 146 optimal weight:    1.9990
   chunk 131 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0970
   chunk 88 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 136 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 101 optimal weight:    6.9990
   chunk 158 optimal weight:    5.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 316 HIS
** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 127 HIS
** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 382 GLN
E 397 HIS
** D  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 297 HIS
B 156 HIS
B 243 HIS
B 624 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.052080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.038958 restraints weight = 81378.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.040261 restraints weight = 40037.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.041099 restraints weight = 26091.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14312  Z= 0.132
  Angle     :  0.610   7.552  19390  Z= 0.320
  Chirality :  0.043   0.201   2121
  Planarity :  0.004   0.072   2499
  Dihedral  :  4.751  27.882   1880
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.81 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.18 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.20), residues: 1719
  helix:  1.18 (0.28), residues: 356
  sheet: -0.92 (0.26), residues: 409
  loop : -2.01 (0.19), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 364 
 HIS   0.006   0.001   HIS D 297 
 PHE   0.026   0.001   PHE D  32 
 TYR   0.019   0.001   TYR B 434 
 ARG   0.004   0.000   ARG E 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 (  443)
  hydrogen bonds       : angle       5.35342 ( 1260)
  SS BOND              : bond        0.00459 (    6)
  SS BOND              : angle       1.47214 (   12)
  covalent geometry    : bond        0.00286 (14306)
  covalent geometry    : angle       0.60952 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 73
  time to evaluate  : 1.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6886 (p0)
REVERT: A  253 MET cc_start: 0.7628 (ttp) cc_final: 0.7263 (mtm)
REVERT: A  342 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9152 (tt)
REVERT: E  308 TYR cc_start: 0.7322 (m-10) cc_final: 0.7109 (m-10)
REVERT: D  439 MET cc_start: 0.9560 (ttp) cc_final: 0.8832 (tmm)
REVERT: B  244 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7884 (mtp)
REVERT: B  299 MET cc_start: 0.9382 (ttm) cc_final: 0.9035 (tpp)
  outliers start: 43
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1950
  time to fit residues: 35.9410
Evaluate side-chains
  87 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 1.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain C residue  419 ILE
Chi-restraints excluded: chain C residue  484 THR
Chi-restraints excluded: chain E residue  376 MET
Chi-restraints excluded: chain E residue  395 ASP
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  547 CYS
Chi-restraints excluded: chain D residue  635 ASN
Chi-restraints excluded: chain D residue  659 ASP
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain B residue  481 HIS
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  596 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 75 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 160 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 153 optimal weight:    0.8980
   chunk 151 optimal weight:    5.9990
   chunk 146 optimal weight:   20.0000
   chunk 7 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 HIS
D  45 ASN
B 449 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.051199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.037923 restraints weight = 82115.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.039186 restraints weight = 40828.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.039993 restraints weight = 26947.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2912
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2912
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14312  Z= 0.135
  Angle     :  0.572   7.872  19390  Z= 0.300
  Chirality :  0.043   0.201   2121
  Planarity :  0.004   0.062   2499
  Dihedral  :  4.554  24.872   1880
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.86 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.39 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.20), residues: 1719
  helix:  1.33 (0.28), residues: 358
  sheet: -0.79 (0.26), residues: 405
  loop : -1.90 (0.19), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 361 
 HIS   0.022   0.001   HIS B 243 
 PHE   0.021   0.001   PHE D  32 
 TYR   0.009   0.001   TYR C 493 
 ARG   0.004   0.000   ARG D 685 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  443)
  hydrogen bonds       : angle       4.97180 ( 1260)
  SS BOND              : bond        0.00404 (    6)
  SS BOND              : angle       1.23084 (   12)
  covalent geometry    : bond        0.00298 (14306)
  covalent geometry    : angle       0.57157 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 69
  time to evaluate  : 1.765 
Fit side-chains
REVERT: A  253 MET cc_start: 0.7798 (ttp) cc_final: 0.7397 (mtm)
REVERT: A  342 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9202 (tt)
REVERT: C  438 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8089 (ptm160)
REVERT: C  454 GLU cc_start: 0.8366 (pp20) cc_final: 0.8088 (pp20)
REVERT: E  252 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8465 (tpt)
REVERT: D  110 MET cc_start: 0.9169 (ttt) cc_final: 0.8799 (ttt)
REVERT: D  439 MET cc_start: 0.9556 (ttp) cc_final: 0.8849 (tmm)
REVERT: B  244 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7835 (mtp)
REVERT: B  299 MET cc_start: 0.9392 (ttm) cc_final: 0.9050 (tpp)
  outliers start: 50
  outliers final: 19
  residues processed: 111
  average time/residue: 0.2183
  time to fit residues: 39.2252
Evaluate side-chains
  87 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 1.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain C residue  419 ILE
Chi-restraints excluded: chain C residue  438 ARG
Chi-restraints excluded: chain C residue  462 VAL
Chi-restraints excluded: chain C residue  484 THR
Chi-restraints excluded: chain E residue  252 MET
Chi-restraints excluded: chain E residue  376 MET
Chi-restraints excluded: chain E residue  395 ASP
Chi-restraints excluded: chain E residue  404 LEU
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  443 LEU
Chi-restraints excluded: chain D residue  547 CYS
Chi-restraints excluded: chain D residue  594 TRP
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  657 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 85 optimal weight:   40.0000
   chunk 57 optimal weight:    1.9990
   chunk 167 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   chunk 168 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 300 HIS
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.050708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.037535 restraints weight = 81384.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.038765 restraints weight = 40474.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.039543 restraints weight = 26653.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2889
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
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      :  0.003   0.037  14312  Z= 0.130
  Angle     :  0.568   8.669  19390  Z= 0.293
  Chirality :  0.043   0.183   2121
  Planarity :  0.004   0.061   2499
  Dihedral  :  4.410  21.530   1880
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.81 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.92 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.20), residues: 1719
  helix:  1.48 (0.28), residues: 359
  sheet: -0.59 (0.26), residues: 407
  loop : -1.76 (0.19), residues: 953

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 361 
 HIS   0.006   0.001   HIS D 706 
 PHE   0.017   0.001   PHE D  32 
 TYR   0.012   0.001   TYR B 480 
 ARG   0.004   0.000   ARG D 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  443)
  hydrogen bonds       : angle       4.72758 ( 1260)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       1.25398 (   12)
  covalent geometry    : bond        0.00289 (14306)
  covalent geometry    : angle       0.56741 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 67
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6877 (p0)
REVERT: A  253 MET cc_start: 0.7949 (ttp) cc_final: 0.7466 (mtm)
REVERT: A  342 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9275 (tt)
REVERT: C  438 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8147 (ptm160)
REVERT: C  454 GLU cc_start: 0.8429 (pp20) cc_final: 0.8116 (pp20)
REVERT: E  252 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8530 (tpt)
REVERT: E  308 TYR cc_start: 0.7253 (m-10) cc_final: 0.7036 (m-10)
REVERT: D  110 MET cc_start: 0.9253 (ttt) cc_final: 0.8701 (ttt)
REVERT: D  439 MET cc_start: 0.9552 (ttp) cc_final: 0.8839 (tmm)
REVERT: D  701 MET cc_start: 0.8409 (tpp) cc_final: 0.7920 (tpp)
REVERT: B  244 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7926 (mtp)
REVERT: B  299 MET cc_start: 0.9385 (ttm) cc_final: 0.9018 (tpp)
  outliers start: 42
  outliers final: 21
  residues processed: 102
  average time/residue: 0.2044
  time to fit residues: 34.2409
Evaluate side-chains
  91 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 65
  time to evaluate  : 1.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  176 HIS
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain C residue  438 ARG
Chi-restraints excluded: chain C residue  462 VAL
Chi-restraints excluded: chain C residue  484 THR
Chi-restraints excluded: chain E residue  232 VAL
Chi-restraints excluded: chain E residue  252 MET
Chi-restraints excluded: chain E residue  376 MET
Chi-restraints excluded: chain E residue  395 ASP
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  443 LEU
Chi-restraints excluded: chain D residue  547 CYS
Chi-restraints excluded: chain D residue  594 TRP
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  596 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 131 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 149 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 80 optimal weight:    4.9990
   chunk 155 optimal weight:   10.0000
   chunk 158 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 151 optimal weight:    3.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 469 GLN
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.049813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.036490 restraints weight = 83350.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.037706 restraints weight = 41470.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.038487 restraints weight = 27369.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14312  Z= 0.146
  Angle     :  0.576  12.368  19390  Z= 0.294
  Chirality :  0.042   0.208   2121
  Planarity :  0.004   0.061   2499
  Dihedral  :  4.362  21.511   1880
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.86 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.31 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.20), residues: 1719
  helix:  1.56 (0.28), residues: 360
  sheet: -0.50 (0.27), residues: 395
  loop : -1.67 (0.19), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 361 
 HIS   0.005   0.001   HIS D 297 
 PHE   0.013   0.001   PHE A 243 
 TYR   0.012   0.001   TYR E 244 
 ARG   0.009   0.000   ARG D 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  443)
  hydrogen bonds       : angle       4.59145 ( 1260)
  SS BOND              : bond        0.00303 (    6)
  SS BOND              : angle       1.30991 (   12)
  covalent geometry    : bond        0.00325 (14306)
  covalent geometry    : angle       0.57536 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 65
  time to evaluate  : 1.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6942 (p0)
REVERT: A  253 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7737 (mtm)
REVERT: A  342 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9287 (tt)
REVERT: C  454 GLU cc_start: 0.8456 (pp20) cc_final: 0.8133 (pp20)
REVERT: E  252 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8568 (tpt)
REVERT: E  271 MET cc_start: 0.8524 (mpp) cc_final: 0.8319 (mpp)
REVERT: D  110 MET cc_start: 0.9282 (ttt) cc_final: 0.8677 (ttt)
REVERT: D  439 MET cc_start: 0.9539 (ttp) cc_final: 0.8834 (tmm)
REVERT: D  701 MET cc_start: 0.8460 (tpp) cc_final: 0.8054 (tpp)
REVERT: B  244 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8036 (mtp)
REVERT: B  299 MET cc_start: 0.9374 (ttm) cc_final: 0.9004 (tpp)
  outliers start: 39
  outliers final: 25
  residues processed: 93
  average time/residue: 0.2001
  time to fit residues: 30.8301
Evaluate side-chains
  94 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 64
  time to evaluate  : 1.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  176 HIS
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain C residue  438 ARG
Chi-restraints excluded: chain C residue  455 ASP
Chi-restraints excluded: chain C residue  462 VAL
Chi-restraints excluded: chain C residue  484 THR
Chi-restraints excluded: chain E residue  232 VAL
Chi-restraints excluded: chain E residue  252 MET
Chi-restraints excluded: chain E residue  278 TYR
Chi-restraints excluded: chain E residue  395 ASP
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  443 LEU
Chi-restraints excluded: chain D residue  547 CYS
Chi-restraints excluded: chain D residue  594 TRP
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  614 MET
Chi-restraints excluded: chain B residue  657 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 139 optimal weight:    2.9990
   chunk 131 optimal weight:    2.9990
   chunk 146 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.049752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.036517 restraints weight = 83612.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.037691 restraints weight = 41213.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.038456 restraints weight = 27242.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14312  Z= 0.124
  Angle     :  0.548  10.400  19390  Z= 0.281
  Chirality :  0.042   0.188   2121
  Planarity :  0.004   0.058   2499
  Dihedral  :  4.261  21.358   1880
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.69 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 19.71 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.21), residues: 1719
  helix:  1.65 (0.28), residues: 366
  sheet: -0.45 (0.26), residues: 409
  loop : -1.60 (0.20), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 361 
 HIS   0.005   0.001   HIS A 176 
 PHE   0.012   0.001   PHE A 243 
 TYR   0.028   0.001   TYR E  80 
 ARG   0.004   0.000   ARG B 682 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03430 (  443)
  hydrogen bonds       : angle       4.40296 ( 1260)
  SS BOND              : bond        0.00320 (    6)
  SS BOND              : angle       1.27759 (   12)
  covalent geometry    : bond        0.00277 (14306)
  covalent geometry    : angle       0.54702 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 63
  time to evaluate  : 1.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6932 (p0)
REVERT: A  253 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7764 (mtm)
REVERT: A  342 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9269 (tt)
REVERT: C  454 GLU cc_start: 0.8448 (pp20) cc_final: 0.8083 (pp20)
REVERT: D  110 MET cc_start: 0.9298 (ttt) cc_final: 0.8709 (ttt)
REVERT: D  439 MET cc_start: 0.9546 (ttp) cc_final: 0.8847 (tmm)
REVERT: D  701 MET cc_start: 0.8455 (tpp) cc_final: 0.8070 (tpp)
REVERT: B  244 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8009 (mtp)
REVERT: B  299 MET cc_start: 0.9388 (ttm) cc_final: 0.8991 (tpp)
  outliers start: 40
  outliers final: 22
  residues processed: 91
  average time/residue: 0.2027
  time to fit residues: 30.4952
Evaluate side-chains
  87 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 1.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  176 HIS
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain C residue  395 HIS
Chi-restraints excluded: chain C residue  408 HIS
Chi-restraints excluded: chain C residue  438 ARG
Chi-restraints excluded: chain C residue  462 VAL
Chi-restraints excluded: chain C residue  484 THR
Chi-restraints excluded: chain E residue  232 VAL
Chi-restraints excluded: chain E residue  278 TYR
Chi-restraints excluded: chain E residue  395 ASP
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  443 LEU
Chi-restraints excluded: chain D residue  547 CYS
Chi-restraints excluded: chain D residue  594 TRP
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  657 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 149 optimal weight:    4.9990
   chunk 172 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 157 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 148 optimal weight:    7.9990
   chunk 115 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 456 ASN
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.049541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.036337 restraints weight = 82976.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.037507 restraints weight = 40874.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.038273 restraints weight = 26951.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14312  Z= 0.121
  Angle     :  0.552  11.418  19390  Z= 0.282
  Chirality :  0.042   0.184   2121
  Planarity :  0.004   0.059   2499
  Dihedral  :  4.182  21.300   1880
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.52 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.78 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.21), residues: 1719
  helix:  1.71 (0.28), residues: 366
  sheet: -0.34 (0.27), residues: 408
  loop : -1.52 (0.20), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 361 
 HIS   0.005   0.001   HIS A 176 
 PHE   0.012   0.001   PHE A 243 
 TYR   0.025   0.001   TYR E  80 
 ARG   0.005   0.000   ARG D 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03447 (  443)
  hydrogen bonds       : angle       4.36502 ( 1260)
  SS BOND              : bond        0.00313 (    6)
  SS BOND              : angle       1.26060 (   12)
  covalent geometry    : bond        0.00270 (14306)
  covalent geometry    : angle       0.55160 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 61
  time to evaluate  : 1.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6836 (p0)
REVERT: A  253 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7763 (mtm)
REVERT: A  342 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9249 (tt)
REVERT: C  454 GLU cc_start: 0.8434 (pp20) cc_final: 0.8113 (pp20)
REVERT: E  271 MET cc_start: 0.8637 (mpp) cc_final: 0.8388 (mpp)
REVERT: D  110 MET cc_start: 0.9308 (ttt) cc_final: 0.8700 (ttt)
REVERT: D  439 MET cc_start: 0.9543 (ttp) cc_final: 0.8799 (ppp)
REVERT: D  701 MET cc_start: 0.8451 (tpp) cc_final: 0.8088 (tpp)
REVERT: B  244 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7583 (mmm)
REVERT: B  299 MET cc_start: 0.9383 (ttm) cc_final: 0.8979 (tpp)
  outliers start: 39
  outliers final: 24
  residues processed: 89
  average time/residue: 0.2105
  time to fit residues: 31.3833
Evaluate side-chains
  89 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 61
  time to evaluate  : 1.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  176 HIS
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain C residue  395 HIS
Chi-restraints excluded: chain C residue  438 ARG
Chi-restraints excluded: chain C residue  455 ASP
Chi-restraints excluded: chain C residue  462 VAL
Chi-restraints excluded: chain C residue  484 THR
Chi-restraints excluded: chain E residue  232 VAL
Chi-restraints excluded: chain E residue  278 TYR
Chi-restraints excluded: chain E residue  395 ASP
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  443 LEU
Chi-restraints excluded: chain D residue  547 CYS
Chi-restraints excluded: chain D residue  594 TRP
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  657 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 26 optimal weight:    0.0370
   chunk 31 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 167 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 161 optimal weight:    9.9990
   chunk 169 optimal weight:    3.9990
   chunk 127 optimal weight:   10.0000
   chunk 100 optimal weight:    7.9990
   chunk 140 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    2.6064

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 176 ASN
D 521 GLN
B  95 GLN
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.048628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.035386 restraints weight = 82681.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.036549 restraints weight = 41406.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.037282 restraints weight = 27544.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14312  Z= 0.174
  Angle     :  0.588  12.404  19390  Z= 0.299
  Chirality :  0.042   0.185   2121
  Planarity :  0.004   0.061   2499
  Dihedral  :  4.298  23.658   1880
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.81 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.71 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.21), residues: 1719
  helix:  1.76 (0.29), residues: 365
  sheet: -0.17 (0.27), residues: 404
  loop : -1.55 (0.20), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 361 
 HIS   0.006   0.001   HIS A 176 
 PHE   0.011   0.001   PHE A 243 
 TYR   0.025   0.001   TYR E  80 
 ARG   0.003   0.000   ARG D 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  443)
  hydrogen bonds       : angle       4.47424 ( 1260)
  SS BOND              : bond        0.00304 (    6)
  SS BOND              : angle       1.43256 (   12)
  covalent geometry    : bond        0.00388 (14306)
  covalent geometry    : angle       0.58691 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 60
  time to evaluate  : 1.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7010 (p0)
REVERT: A  253 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7925 (mtm)
REVERT: A  342 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9256 (tt)
REVERT: C  454 GLU cc_start: 0.8435 (pp20) cc_final: 0.8112 (pp20)
REVERT: E  271 MET cc_start: 0.8560 (mpp) cc_final: 0.8311 (mpp)
REVERT: D  110 MET cc_start: 0.9276 (ttt) cc_final: 0.8664 (ttt)
REVERT: D  439 MET cc_start: 0.9554 (ttp) cc_final: 0.8823 (ppp)
REVERT: D  701 MET cc_start: 0.8467 (tpp) cc_final: 0.8133 (tpp)
REVERT: B  144 MET cc_start: 0.8948 (tmm) cc_final: 0.8618 (tmm)
REVERT: B  244 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7596 (mmm)
REVERT: B  299 MET cc_start: 0.9340 (ttm) cc_final: 0.8897 (tpp)
  outliers start: 36
  outliers final: 22
  residues processed: 88
  average time/residue: 0.2109
  time to fit residues: 30.9084
Evaluate side-chains
  86 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 60
  time to evaluate  : 1.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  176 HIS
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain C residue  438 ARG
Chi-restraints excluded: chain C residue  455 ASP
Chi-restraints excluded: chain C residue  462 VAL
Chi-restraints excluded: chain C residue  484 THR
Chi-restraints excluded: chain E residue  278 TYR
Chi-restraints excluded: chain E residue  348 SER
Chi-restraints excluded: chain E residue  395 ASP
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  443 LEU
Chi-restraints excluded: chain D residue  547 CYS
Chi-restraints excluded: chain D residue  594 TRP
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  657 MET
Chi-restraints excluded: chain B residue  669 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 161 optimal weight:    0.0040
   chunk 65 optimal weight:    0.8980
   chunk 118 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 135 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 39 optimal weight:    0.0870
   chunk 131 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.4972

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 374 GLN
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.049818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.036577 restraints weight = 82279.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.037789 restraints weight = 40621.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.038561 restraints weight = 26788.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  14312  Z= 0.093
  Angle     :  0.548  12.431  19390  Z= 0.276
  Chirality :  0.042   0.166   2121
  Planarity :  0.004   0.063   2499
  Dihedral  :  4.112  20.155   1880
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.93 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 20.24 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.21), residues: 1719
  helix:  1.71 (0.28), residues: 367
  sheet: -0.17 (0.27), residues: 413
  loop : -1.42 (0.20), residues: 939

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 361 
 HIS   0.005   0.001   HIS A 176 
 PHE   0.012   0.001   PHE A 243 
 TYR   0.020   0.001   TYR E  80 
 ARG   0.004   0.000   ARG D 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03208 (  443)
  hydrogen bonds       : angle       4.24598 ( 1260)
  SS BOND              : bond        0.00386 (    6)
  SS BOND              : angle       1.20887 (   12)
  covalent geometry    : bond        0.00205 (14306)
  covalent geometry    : angle       0.54730 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 63
  time to evaluate  : 1.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6897 (p0)
REVERT: A  253 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7802 (mtm)
REVERT: A  342 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9227 (tt)
REVERT: C  454 GLU cc_start: 0.8441 (pp20) cc_final: 0.8125 (pp20)
REVERT: E  271 MET cc_start: 0.8554 (mpp) cc_final: 0.8276 (mpp)
REVERT: D  110 MET cc_start: 0.9328 (ttt) cc_final: 0.8705 (ttt)
REVERT: D  439 MET cc_start: 0.9546 (ttp) cc_final: 0.8793 (ppp)
REVERT: D  701 MET cc_start: 0.8384 (tpp) cc_final: 0.8003 (tpp)
REVERT: B  144 MET cc_start: 0.8973 (tmm) cc_final: 0.8651 (tmm)
REVERT: B  244 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8050 (mtp)
REVERT: B  299 MET cc_start: 0.9384 (ttm) cc_final: 0.8944 (tpp)
  outliers start: 27
  outliers final: 17
  residues processed: 82
  average time/residue: 0.2156
  time to fit residues: 29.4323
Evaluate side-chains
  82 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 1.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  176 HIS
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain C residue  408 HIS
Chi-restraints excluded: chain C residue  438 ARG
Chi-restraints excluded: chain C residue  455 ASP
Chi-restraints excluded: chain E residue  232 VAL
Chi-restraints excluded: chain E residue  278 TYR
Chi-restraints excluded: chain E residue  395 ASP
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  443 LEU
Chi-restraints excluded: chain D residue  547 CYS
Chi-restraints excluded: chain D residue  594 TRP
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  657 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 100 optimal weight:   10.0000
   chunk 120 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 75 optimal weight:    6.9990
   chunk 106 optimal weight:   20.0000
   chunk 171 optimal weight:    0.9990
   chunk 117 optimal weight:    0.0470
   chunk 56 optimal weight:    5.9990
   chunk 118 optimal weight:    9.9990
   chunk 26 optimal weight:    0.3980
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.0282

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.049589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.036400 restraints weight = 82797.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.037582 restraints weight = 40844.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.038340 restraints weight = 26963.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  14312  Z= 0.101
  Angle     :  0.547  12.479  19390  Z= 0.274
  Chirality :  0.042   0.172   2121
  Planarity :  0.004   0.062   2499
  Dihedral  :  4.016  20.298   1880
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.52 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 20.77 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.21), residues: 1719
  helix:  1.76 (0.28), residues: 367
  sheet: -0.07 (0.27), residues: 411
  loop : -1.37 (0.20), residues: 941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 361 
 HIS   0.005   0.001   HIS A 176 
 PHE   0.012   0.001   PHE A 243 
 TYR   0.021   0.001   TYR E  80 
 ARG   0.003   0.000   ARG D 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03140 (  443)
  hydrogen bonds       : angle       4.18002 ( 1260)
  SS BOND              : bond        0.00341 (    6)
  SS BOND              : angle       1.18733 (   12)
  covalent geometry    : bond        0.00228 (14306)
  covalent geometry    : angle       0.54613 (19378)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 1.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6852 (p0)
REVERT: A  253 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7825 (mtm)
REVERT: A  342 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9248 (tt)
REVERT: C  454 GLU cc_start: 0.8447 (pp20) cc_final: 0.8137 (pp20)
REVERT: E  271 MET cc_start: 0.8570 (mpp) cc_final: 0.8294 (mpp)
REVERT: D  110 MET cc_start: 0.9325 (ttt) cc_final: 0.8717 (ttt)
REVERT: D  439 MET cc_start: 0.9524 (ttp) cc_final: 0.8797 (ppp)
REVERT: D  701 MET cc_start: 0.8375 (tpp) cc_final: 0.8005 (tpp)
REVERT: B  144 MET cc_start: 0.8959 (tmm) cc_final: 0.8630 (tmm)
REVERT: B  244 MET cc_start: 0.8304 (ttp) cc_final: 0.8050 (mtp)
REVERT: B  299 MET cc_start: 0.9394 (ttm) cc_final: 0.8946 (tpp)
  outliers start: 21
  outliers final: 18
  residues processed: 79
  average time/residue: 0.2249
  time to fit residues: 28.6774
Evaluate side-chains
  82 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 1.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  176 HIS
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain C residue  408 HIS
Chi-restraints excluded: chain C residue  438 ARG
Chi-restraints excluded: chain C residue  455 ASP
Chi-restraints excluded: chain E residue  232 VAL
Chi-restraints excluded: chain E residue  278 TYR
Chi-restraints excluded: chain E residue  395 ASP
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  443 LEU
Chi-restraints excluded: chain D residue  547 CYS
Chi-restraints excluded: chain D residue  594 TRP
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  657 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 106 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 61 optimal weight:    0.5980
   chunk 153 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 139 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.049209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.035878 restraints weight = 84596.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.037049 restraints weight = 42098.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.037801 restraints weight = 27962.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14312  Z= 0.115
  Angle     :  0.541  12.395  19390  Z= 0.273
  Chirality :  0.042   0.165   2121
  Planarity :  0.004   0.062   2499
  Dihedral  :  4.016  20.935   1880
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.22 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 20.63 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.21), residues: 1719
  helix:  1.84 (0.28), residues: 366
  sheet: -0.02 (0.27), residues: 409
  loop : -1.36 (0.20), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 361 
 HIS   0.005   0.001   HIS A 176 
 PHE   0.011   0.001   PHE A 243 
 TYR   0.019   0.001   TYR E  80 
 ARG   0.003   0.000   ARG D 685 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03236 (  443)
  hydrogen bonds       : angle       4.18232 ( 1260)
  SS BOND              : bond        0.00347 (    6)
  SS BOND              : angle       1.24824 (   12)
  covalent geometry    : bond        0.00261 (14306)
  covalent geometry    : angle       0.54000 (19378)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4308.46 seconds
wall clock time: 77 minutes 29.05 seconds (4649.05 seconds total)