Starting phenix.real_space_refine
on Mon Mar 11 06:46:59 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b00_11952/03_2024/7b00_11952_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b00_11952/03_2024/7b00_11952.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b00_11952/03_2024/7b00_11952.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b00_11952/03_2024/7b00_11952.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b00_11952/03_2024/7b00_11952_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b00_11952/03_2024/7b00_11952_updated.pdb"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      27      5.16       5
     C    4833      2.51       5
     N    1179      2.21       5
     O    1350      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  122": "NH1" <-> "NH2"
    Residue "A ARG  162": "NH1" <-> "NH2"
    Residue "A ARG  181": "NH1" <-> "NH2"
    Residue "A GLU  257": "OE1" <-> "OE2"
    Residue "A ARG  267": "NH1" <-> "NH2"
    Residue "A GLU  308": "OE1" <-> "OE2"
    Residue "A ARG  361": "NH1" <-> "NH2"
    Residue "A ARG  418": "NH1" <-> "NH2"
    Residue "B GLU   67": "OE1" <-> "OE2"
    Residue "B ARG   79": "NH1" <-> "NH2"
    Residue "B ARG   81": "NH1" <-> "NH2"
    Residue "B ARG  108": "NH1" <-> "NH2"
    Residue "B ARG  110": "NH1" <-> "NH2"
    Residue "B GLU  214": "OE1" <-> "OE2"
    Residue "B GLU  271": "OE1" <-> "OE2"
    Residue "B GLU  432": "OE1" <-> "OE2"
    Residue "B ARG  433": "NH1" <-> "NH2"
    Residue "B GLU  504": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 7389
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3542
          Classifications: {'peptide': 457}
          Link IDs: {'PTRANS': 25, 'TRANS': 431}
    Chain: "B"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 85
          Unusual residues: {'AJP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.55, per 1000 atoms: 0.62
  Number of scatterers: 7389
  At special positions: 0
  Unit cell: (81.6, 77.35, 129.2, 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      27     16.00
     O    1350      8.00
     N    1179      7.00
     C    4833      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS B 109 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN B 405 "
      " NAG D   1 " - " ASN B 264 "
      " NAG E   1 " - " ASN B 280 "
      " NAG F   1 " - " ASN B 323 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.00
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      39 helices and 3 sheets defined
      41.9% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 53
      removed outlier: 3.585A  pdb=" N   ILE A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ILE A  49 " --> pdb=" O   ALA A  45 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   ASN A  52 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 67
      No H-bonds generated for 'chain 'A' and resid 64 through 67'
    Processing helix  chain 'A' and resid 74 through 99
      removed outlier: 3.552A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   TRP A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLY A  83 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A  86 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLU A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR A  99 " --> pdb=" O   GLU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 110
      removed outlier: 3.971A  pdb=" N   VAL A 110 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 125
      removed outlier: 3.984A  pdb=" N   ARG A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU A 123 " --> pdb=" O   GLY A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 147
      removed outlier: 3.562A  pdb=" N   ASN A 144 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR A 145 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 177
      removed outlier: 3.977A  pdb=" N   ARG A 162 " --> pdb=" O   GLU A 158 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   LEU A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LEU A 164 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ILE A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   CYS A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LEU A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TRP A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 185
      removed outlier: 3.674A  pdb=" N   THR A 184 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ARG A 185 " --> pdb=" O   TRP A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 190
      No H-bonds generated for 'chain 'A' and resid 187 through 190'
    Processing helix  chain 'A' and resid 192 through 210
      removed outlier: 3.993A  pdb=" N   ILE A 206 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 259
      No H-bonds generated for 'chain 'A' and resid 256 through 259'
    Processing helix  chain 'A' and resid 273 through 288
      removed outlier: 3.728A  pdb=" N   VAL A 279 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 285 " --> pdb=" O   VAL A 281 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL A 288 " --> pdb=" O   ASN A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 308
    Processing helix  chain 'A' and resid 318 through 323
      removed outlier: 3.754A  pdb=" N   ALA A 323 " --> pdb=" O   PRO A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 344
      removed outlier: 4.625A  pdb=" N   PHE A 342 " --> pdb=" O   ARG A 339 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA A 343 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 379
      removed outlier: 3.586A  pdb=" N   LEU A 369 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   PHE A 370 " --> pdb=" O   PRO A 366 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   THR A 371 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU A 376 " --> pdb=" O   CYS A 372 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   MET A 378 " --> pdb=" O   SER A 374 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 379 " --> pdb=" O   THR A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 411
      removed outlier: 3.828A  pdb=" N   ASN A 389 " --> pdb=" O   TYR A 385 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR A 390 " --> pdb=" O   THR A 386 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ILE A 394 " --> pdb=" O   TYR A 390 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE A 398 " --> pdb=" O   ILE A 394 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLY A 400 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   THR A 402 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   VAL A 403 " --> pdb=" O   TYR A 399 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   GLN A 406 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 433
      removed outlier: 3.556A  pdb=" N   TYR A 430 " --> pdb=" O   PHE A 426 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LEU A 431 " --> pdb=" O   PRO A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 443
      removed outlier: 3.659A  pdb=" N   PHE A 440 " --> pdb=" O   PHE A 436 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   SER A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TRP A 443 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 455
      No H-bonds generated for 'chain 'A' and resid 452 through 455'
    Processing helix  chain 'A' and resid 458 through 464
      removed outlier: 3.522A  pdb=" N   PHE A 464 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 490
      removed outlier: 3.688A  pdb=" N   ILE A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   THR A 484 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A 485 " --> pdb=" O   GLU A 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 72
      removed outlier: 3.687A  pdb=" N   VAL B  71 " --> pdb=" O   GLU B  67 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B  72 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 105
      removed outlier: 3.868A  pdb=" N   ARG B  79 " --> pdb=" O   PRO B  75 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR B  80 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   TRP B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   MET B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   GLY B  98 " --> pdb=" O   GLY B  94 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA B  99 " --> pdb=" O   MET B  95 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE B 102 " --> pdb=" O   GLY B  98 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL B 104 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 119
      No H-bonds generated for 'chain 'B' and resid 117 through 119'
    Processing helix  chain 'B' and resid 129 through 133
      removed outlier: 3.729A  pdb=" N   GLN B 133 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 129 through 133'
    Processing helix  chain 'B' and resid 140 through 145
      removed outlier: 3.898A  pdb=" N   LYS B 144 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY B 145 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 150
      No H-bonds generated for 'chain 'B' and resid 147 through 150'
    Processing helix  chain 'B' and resid 186 through 196
      removed outlier: 3.570A  pdb=" N   SER B 191 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   SER B 195 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 227
      No H-bonds generated for 'chain 'B' and resid 224 through 227'
    Processing helix  chain 'B' and resid 229 through 239
      removed outlier: 3.701A  pdb=" N   GLU B 234 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LEU B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA B 239 " --> pdb=" O   PHE B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 269
      removed outlier: 3.502A  pdb=" N   TRP B 262 " --> pdb=" O   PHE B 258 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ILE B 265 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 290
      removed outlier: 3.573A  pdb=" N   LEU B 288 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 325
      removed outlier: 3.561A  pdb=" N   THR B 325 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 356
      removed outlier: 3.845A  pdb=" N   LEU B 349 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   ARG B 350 " --> pdb=" O   GLN B 347 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   GLN B 353 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU B 356 " --> pdb=" O   GLN B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 406
      No H-bonds generated for 'chain 'B' and resid 404 through 406'
    Processing helix  chain 'B' and resid 408 through 411
      No H-bonds generated for 'chain 'B' and resid 408 through 411'
    Processing helix  chain 'B' and resid 419 through 426
    Processing helix  chain 'B' and resid 434 through 437
      No H-bonds generated for 'chain 'B' and resid 434 through 437'
    Processing sheet with id=  A, first strand: chain 'B' and resid 123 through 125
    Processing sheet with id=  B, first strand: chain 'B' and resid 244 through 247
      removed outlier: 6.461A  pdb=" N   LEU B 298 " --> pdb=" O   ALA B 277 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 439 through 442
      removed outlier: 3.632A  pdb=" N   VAL B 465 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLU B 519 " --> pdb=" O   ASN B 467 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU B 496 " --> pdb=" O   LEU B 522 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ARG B 524 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   LEU B 494 " --> pdb=" O   ARG B 524 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU B 508 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    504 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 3.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2204
        1.34 -     1.46: 1444
        1.46 -     1.57: 3894
        1.57 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 7583
  Sorted by residual:
  bond pdb=" C56 AJP A 601 "
       pdb=" C57 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.522  1.558 -0.036 2.00e-02 2.50e+03 3.24e+00
  bond pdb=" C65 AJP A 601 "
       pdb=" O64 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.373  1.408 -0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" C57 AJP A 601 "
       pdb=" O64 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.414  1.443 -0.029 2.00e-02 2.50e+03 2.17e+00
  bond pdb=" C3  NAG F   1 "
       pdb=" O3  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.432 -0.029 2.00e-02 2.50e+03 2.16e+00
  bond pdb=" C3  NAG D   2 "
       pdb=" O3  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.432 -0.029 2.00e-02 2.50e+03 2.08e+00
  ... (remaining 7578 not shown)

  Histogram of bond angle deviations from ideal:
       98.45 -   105.60: 188
      105.60 -   112.76: 4043
      112.76 -   119.92: 2786
      119.92 -   127.08: 3217
      127.08 -   134.23: 116
  Bond angle restraints: 10350
  Sorted by residual:
  angle pdb=" N   ARG B 433 "
        pdb=" CA  ARG B 433 "
        pdb=" C   ARG B 433 "
      ideal   model   delta    sigma   weight residual
     114.56  108.83    5.73 1.27e+00 6.20e-01 2.04e+01
  angle pdb=" C   PRO A 364 "
        pdb=" N   ILE A 365 "
        pdb=" CA  ILE A 365 "
      ideal   model   delta    sigma   weight residual
     120.33  123.54   -3.21 8.00e-01 1.56e+00 1.61e+01
  angle pdb=" CA  ILE A 365 "
        pdb=" C   ILE A 365 "
        pdb=" N   PRO A 366 "
      ideal   model   delta    sigma   weight residual
     120.83  123.17   -2.34 6.10e-01 2.69e+00 1.47e+01
  angle pdb=" C   ASP A 230 "
        pdb=" N   ILE A 231 "
        pdb=" CA  ILE A 231 "
      ideal   model   delta    sigma   weight residual
     121.97  128.74   -6.77 1.80e+00 3.09e-01 1.41e+01
  angle pdb=" C   SER A 444 "
        pdb=" N   GLU A 445 "
        pdb=" CA  GLU A 445 "
      ideal   model   delta    sigma   weight residual
     121.80  130.57   -8.77 2.44e+00 1.68e-01 1.29e+01
  ... (remaining 10345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.70: 4376
       24.70 -    49.39: 281
       49.39 -    74.09: 21
       74.09 -    98.79: 3
       98.79 -   123.48: 17
  Dihedral angle restraints: 4698
    sinusoidal: 2050
      harmonic: 2648
  Sorted by residual:
  dihedral pdb=" CB  CYS A 154 "
           pdb=" SG  CYS A 154 "
           pdb=" SG  CYS B 109 "
           pdb=" CB  CYS B 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -39.60  -46.40     1      1.00e+01 1.00e-02 2.98e+01
  dihedral pdb=" CA  LEU A 350 "
           pdb=" C   LEU A 350 "
           pdb=" N   PRO A 351 "
           pdb=" CA  PRO A 351 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.71  -23.29     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  THR A 133 "
           pdb=" C   THR A 133 "
           pdb=" N   ASN A 134 "
           pdb=" CA  ASN A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.55   22.45     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 4695 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.331: 1231
       0.331 -    0.662: 2
       0.662 -    0.992: 0
       0.992 -    1.323: 0
       1.323 -    1.654: 1
  Chirality restraints: 1234
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN B 323 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.75   -1.65 2.00e-01 2.50e+01 6.84e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 4.04e+01
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.28   -0.12 2.00e-02 2.50e+03 3.41e+01
  ... (remaining 1231 not shown)

  Planarity restraints: 1269
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "   -0.343 2.00e-02 2.50e+03   2.97e-01 1.10e+03
        pdb=" C7  NAG F   1 "    0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "   -0.069 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "    0.524 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "   -0.192 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   2 "   -0.272 2.00e-02 2.50e+03   2.27e-01 6.46e+02
        pdb=" C7  NAG F   2 "    0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG F   2 "   -0.181 2.00e-02 2.50e+03
        pdb=" N2  NAG F   2 "    0.383 2.00e-02 2.50e+03
        pdb=" O7  NAG F   2 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.224 2.00e-02 2.50e+03   1.91e-01 4.55e+02
        pdb=" C7  NAG D   2 "    0.048 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.037 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.313 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.173 2.00e-02 2.50e+03
  ... (remaining 1266 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 33
        2.45 -     3.06: 4172
        3.06 -     3.68: 11086
        3.68 -     4.29: 15345
        4.29 -     4.90: 25022
  Nonbonded interactions: 55658
  Sorted by model distance:
  nonbonded pdb=" O3  NAG D   1 "
            pdb=" O6  NAG D   1 "
     model   vdw
     1.838 2.440
  nonbonded pdb=" O   ILE A 138 "
            pdb=" OG1 THR A 326 "
     model   vdw
     2.241 2.440
  nonbonded pdb=" O   GLY A 332 "
            pdb=" OG1 THR A 336 "
     model   vdw
     2.272 2.440
  nonbonded pdb=" O   SER B 305 "
            pdb=" OG  SER B 305 "
     model   vdw
     2.286 2.440
  nonbonded pdb=" O   SER B 302 "
            pdb=" OG  SER B 302 "
     model   vdw
     2.298 2.440
  ... (remaining 55653 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.870
  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:          11.350
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     23.350
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  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:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
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      :  0.006   0.067   7583  Z= 0.365
  Angle     :  0.968  11.014  10350  Z= 0.494
  Chirality :  0.076   1.654   1234
  Planarity :  0.014   0.297   1265
  Dihedral  : 17.032 123.481   2999
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 12.24 %
    Favored  : 87.37 %
  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: -6.20 (0.17), residues: 922
  helix: -4.76 (0.09), residues: 417
  sheet: -1.62 (0.66), residues: 52
  loop : -3.77 (0.21), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 469 
 HIS   0.007   0.001   HIS A 358 
 PHE   0.022   0.002   PHE A 226 
 TYR   0.022   0.002   TYR A  93 
 ARG   0.004   0.001   ARG A 122 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 159
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ILE cc_start: 0.8369 (pt) cc_final: 0.8114 (mm)
REVERT: A  184 THR cc_start: 0.8873 (t) cc_final: 0.8474 (m)
REVERT: A  211 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7677 (ttpp)
REVERT: A  264 ASN cc_start: 0.7982 (m-40) cc_final: 0.7700 (m-40)
REVERT: A  284 ASN cc_start: 0.8556 (m-40) cc_final: 0.7769 (t0)
REVERT: B  146 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7238 (mmt90)
REVERT: B  187 GLU cc_start: 0.7815 (pm20) cc_final: 0.7584 (pm20)
REVERT: B  432 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7429 (tp30)
  outliers start: 3
  outliers final: 1
  residues processed: 162
  average time/residue: 0.1891
  time to fit residues: 41.1016
Evaluate side-chains
  121 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.0570
   chunk 68 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 23 optimal weight:    0.8980
   chunk 46 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 82 optimal weight:    0.1980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7583  Z= 0.191
  Angle     :  0.700  11.185  10350  Z= 0.336
  Chirality :  0.043   0.352   1234
  Planarity :  0.005   0.045   1265
  Dihedral  : 13.179 105.395   1375
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.53 %
    Favored  : 80.03 %
  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: -4.96 (0.21), residues: 922
  helix: -3.45 (0.17), residues: 425
  sheet: -1.47 (0.68), residues: 52
  loop : -3.35 (0.24), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 358 
 PHE   0.024   0.002   PHE A 155 
 TYR   0.014   0.001   TYR B 303 
 ARG   0.003   0.000   ARG A 339 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ILE cc_start: 0.8181 (pt) cc_final: 0.7976 (mm)
REVERT: A  264 ASN cc_start: 0.7927 (m-40) cc_final: 0.7642 (m-40)
REVERT: A  284 ASN cc_start: 0.8293 (m-40) cc_final: 0.7964 (t0)
REVERT: A  314 MET cc_start: 0.6204 (tpt) cc_final: 0.5743 (tpt)
REVERT: A  346 ARG cc_start: 0.6577 (mpt180) cc_final: 0.6337 (mpt180)
REVERT: B  146 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7257 (mmt90)
REVERT: B  312 GLU cc_start: 0.7065 (pm20) cc_final: 0.6727 (pm20)
REVERT: B  432 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7553 (tp30)
  outliers start: 19
  outliers final: 11
  residues processed: 140
  average time/residue: 0.1851
  time to fit residues: 35.3762
Evaluate side-chains
  122 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  482 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0980
   chunk 66 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7583  Z= 0.228
  Angle     :  0.669  10.410  10350  Z= 0.319
  Chirality :  0.043   0.292   1234
  Planarity :  0.004   0.046   1265
  Dihedral  : 11.814 105.248   1375
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 18.81 %
    Favored  : 76.29 %
  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: -4.21 (0.24), residues: 922
  helix: -2.63 (0.21), residues: 436
  sheet: -1.72 (0.59), residues: 69
  loop : -3.12 (0.27), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 248 
 HIS   0.003   0.001   HIS B 455 
 PHE   0.023   0.002   PHE A 155 
 TYR   0.011   0.001   TYR A  93 
 ARG   0.003   0.000   ARG B 338 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 121
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ILE cc_start: 0.8263 (pt) cc_final: 0.8029 (mm)
REVERT: A  155 PHE cc_start: 0.8009 (p90) cc_final: 0.7711 (p90)
REVERT: A  258 LEU cc_start: 0.0618 (OUTLIER) cc_final: 0.0396 (tt)
REVERT: A  264 ASN cc_start: 0.7763 (m-40) cc_final: 0.7466 (m-40)
REVERT: A  284 ASN cc_start: 0.8296 (m-40) cc_final: 0.8012 (t0)
REVERT: A  314 MET cc_start: 0.6056 (tpt) cc_final: 0.5741 (tpt)
REVERT: A  346 ARG cc_start: 0.6859 (mpt180) cc_final: 0.6587 (mpt180)
REVERT: A  461 PRO cc_start: 0.8423 (Cg_exo) cc_final: 0.8160 (Cg_endo)
REVERT: A  471 HIS cc_start: 0.4049 (OUTLIER) cc_final: 0.2750 (m-70)
REVERT: B  258 PHE cc_start: 0.7628 (m-80) cc_final: 0.7357 (m-80)
REVERT: B  432 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7667 (tp30)
  outliers start: 38
  outliers final: 30
  residues processed: 148
  average time/residue: 0.1708
  time to fit residues: 35.1943
Evaluate side-chains
  147 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  493 ASP
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 39 optimal weight:    0.0170
   chunk 55 optimal weight:    5.9990
   chunk 83 optimal weight:    0.4980
   chunk 87 optimal weight:    0.0970
   chunk 43 optimal weight:    0.0470
   chunk 78 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0570
   chunk 73 optimal weight:    0.0970
   overall best weight:    0.0630

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 ASN
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 GLN
B 381 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7583  Z= 0.132
  Angle     :  0.609   9.928  10350  Z= 0.287
  Chirality :  0.040   0.300   1234
  Planarity :  0.004   0.037   1265
  Dihedral  : 10.322  98.241   1375
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.01 %
    Favored  : 75.64 %
  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: -3.58 (0.25), residues: 922
  helix: -2.00 (0.23), residues: 417
  sheet: -1.51 (0.62), residues: 69
  loop : -2.90 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 117 
 HIS   0.003   0.001   HIS B 437 
 PHE   0.024   0.001   PHE A 433 
 TYR   0.008   0.001   TYR B 367 
 ARG   0.004   0.000   ARG B 146 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.8705 (t) cc_final: 0.8412 (m)
REVERT: A  264 ASN cc_start: 0.7642 (m-40) cc_final: 0.7291 (m-40)
REVERT: A  284 ASN cc_start: 0.8155 (m110) cc_final: 0.7893 (t0)
REVERT: A  411 TRP cc_start: 0.5055 (t-100) cc_final: 0.4828 (t-100)
REVERT: B   89 TRP cc_start: 0.7597 (m100) cc_final: 0.7078 (m100)
REVERT: B  258 PHE cc_start: 0.7615 (m-80) cc_final: 0.7375 (m-80)
REVERT: B  432 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7591 (tp30)
  outliers start: 26
  outliers final: 17
  residues processed: 148
  average time/residue: 0.1659
  time to fit residues: 34.7225
Evaluate side-chains
  137 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  358 THR
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  493 ASP
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0010
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 0 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0070
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.3804

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7583  Z= 0.154
  Angle     :  0.616   9.723  10350  Z= 0.287
  Chirality :  0.042   0.306   1234
  Planarity :  0.003   0.037   1265
  Dihedral  : 10.153  94.714   1375
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 21.01 %
    Favored  : 73.84 %
  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: -3.32 (0.26), residues: 922
  helix: -1.74 (0.24), residues: 423
  sheet: -1.33 (0.63), residues: 69
  loop : -2.83 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 216 
 HIS   0.002   0.001   HIS A 349 
 PHE   0.035   0.001   PHE A 155 
 TYR   0.024   0.001   TYR B 303 
 ARG   0.004   0.000   ARG B 105 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 131
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.8691 (t) cc_final: 0.8425 (m)
REVERT: A  264 ASN cc_start: 0.7632 (m-40) cc_final: 0.7326 (m110)
REVERT: A  284 ASN cc_start: 0.8405 (m110) cc_final: 0.7902 (t0)
REVERT: A  398 PHE cc_start: 0.8307 (m-10) cc_final: 0.7893 (m-10)
REVERT: A  471 HIS cc_start: 0.3888 (OUTLIER) cc_final: 0.2597 (m-70)
REVERT: B  258 PHE cc_start: 0.7640 (m-80) cc_final: 0.6629 (m-80)
REVERT: B  262 TRP cc_start: 0.8959 (m-10) cc_final: 0.8310 (m-90)
REVERT: B  347 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6691 (pp30)
REVERT: B  432 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7674 (tp30)
  outliers start: 40
  outliers final: 33
  residues processed: 158
  average time/residue: 0.1576
  time to fit residues: 35.2460
Evaluate side-chains
  159 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 124
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  347 GLN
Chi-restraints excluded: chain B residue  358 THR
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  460 GLU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  493 ASP
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7583  Z= 0.330
  Angle     :  0.713   9.696  10350  Z= 0.339
  Chirality :  0.047   0.297   1234
  Planarity :  0.004   0.044   1265
  Dihedral  : 10.370  93.059   1375
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 22.04 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.27), residues: 922
  helix: -1.68 (0.24), residues: 435
  sheet: -1.56 (0.62), residues: 70
  loop : -2.70 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 124 
 HIS   0.004   0.001   HIS B 455 
 PHE   0.028   0.002   PHE A 155 
 TYR   0.013   0.002   TYR B 149 
 ARG   0.003   0.000   ARG A 122 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 121
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 TRP cc_start: 0.8288 (OUTLIER) cc_final: 0.7371 (t60)
REVERT: A  130 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8489 (tt)
REVERT: A  184 THR cc_start: 0.8801 (t) cc_final: 0.8515 (m)
REVERT: A  264 ASN cc_start: 0.7638 (m-40) cc_final: 0.7371 (m110)
REVERT: A  284 ASN cc_start: 0.8501 (m110) cc_final: 0.8117 (t0)
REVERT: A  350 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6943 (mp)
REVERT: A  398 PHE cc_start: 0.8439 (m-10) cc_final: 0.8082 (m-10)
REVERT: A  471 HIS cc_start: 0.4142 (OUTLIER) cc_final: 0.2783 (m-70)
REVERT: B  170 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7307 (p0)
REVERT: B  258 PHE cc_start: 0.7669 (m-80) cc_final: 0.6674 (m-80)
REVERT: B  262 TRP cc_start: 0.8981 (m-10) cc_final: 0.8334 (m-90)
  outliers start: 42
  outliers final: 32
  residues processed: 149
  average time/residue: 0.1657
  time to fit residues: 34.6506
Evaluate side-chains
  153 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  124 TRP
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  358 THR
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  460 GLU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  493 ASP
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0370
   chunk 64 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0980
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0060
   chunk 35 optimal weight:    0.2980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.2674

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7583  Z= 0.152
  Angle     :  0.638   9.639  10350  Z= 0.300
  Chirality :  0.042   0.286   1234
  Planarity :  0.003   0.041   1265
  Dihedral  :  9.826  88.276   1375
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.71 %
    Favored  : 71.78 %
  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: -2.90 (0.27), residues: 922
  helix: -1.33 (0.25), residues: 426
  sheet: -1.50 (0.63), residues: 70
  loop : -2.62 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 117 
 HIS   0.003   0.001   HIS A 358 
 PHE   0.029   0.001   PHE A 155 
 TYR   0.022   0.001   TYR B 303 
 ARG   0.004   0.000   ARG B 338 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.8779 (t) cc_final: 0.8502 (m)
REVERT: A  264 ASN cc_start: 0.7595 (m-40) cc_final: 0.7268 (m110)
REVERT: A  284 ASN cc_start: 0.8403 (m110) cc_final: 0.7982 (t0)
REVERT: A  398 PHE cc_start: 0.8336 (m-10) cc_final: 0.7948 (m-10)
REVERT: A  464 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.5478 (m-10)
REVERT: A  471 HIS cc_start: 0.4006 (OUTLIER) cc_final: 0.2651 (m-70)
REVERT: B  258 PHE cc_start: 0.7688 (m-80) cc_final: 0.6705 (m-80)
REVERT: B  262 TRP cc_start: 0.8974 (m-10) cc_final: 0.8336 (m-90)
  outliers start: 35
  outliers final: 22
  residues processed: 148
  average time/residue: 0.1613
  time to fit residues: 33.8857
Evaluate side-chains
  149 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  358 THR
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  493 ASP
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 55 optimal weight:    8.9990
   chunk 59 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0370
   chunk 84 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.9060

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7583  Z= 0.244
  Angle     :  0.672   9.636  10350  Z= 0.315
  Chirality :  0.045   0.287   1234
  Planarity :  0.004   0.045   1265
  Dihedral  :  9.781  85.809   1375
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.97 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -2.88 (0.27), residues: 922
  helix: -1.27 (0.25), residues: 428
  sheet: -1.51 (0.62), residues: 70
  loop : -2.64 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 469 
 HIS   0.003   0.001   HIS A 349 
 PHE   0.025   0.002   PHE A 155 
 TYR   0.017   0.001   TYR A 109 
 ARG   0.003   0.000   ARG B 338 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.8792 (t) cc_final: 0.8504 (m)
REVERT: A  264 ASN cc_start: 0.7639 (m-40) cc_final: 0.7374 (m110)
REVERT: A  284 ASN cc_start: 0.8433 (m110) cc_final: 0.8072 (t0)
REVERT: A  398 PHE cc_start: 0.8404 (m-10) cc_final: 0.8036 (m-10)
REVERT: A  471 HIS cc_start: 0.4140 (OUTLIER) cc_final: 0.2781 (m-70)
REVERT: A  488 GLN cc_start: 0.8162 (mt0) cc_final: 0.7910 (mp10)
REVERT: B  146 ARG cc_start: 0.7916 (mmt180) cc_final: 0.7420 (mpt90)
REVERT: B  170 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7214 (p0)
REVERT: B  258 PHE cc_start: 0.7698 (m-80) cc_final: 0.6723 (m-80)
REVERT: B  262 TRP cc_start: 0.8978 (m-10) cc_final: 0.8356 (m-90)
  outliers start: 35
  outliers final: 29
  residues processed: 149
  average time/residue: 0.1691
  time to fit residues: 35.2780
Evaluate side-chains
  157 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  358 THR
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  493 ASP
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0770
   chunk 73 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7583  Z= 0.209
  Angle     :  0.685  11.035  10350  Z= 0.319
  Chirality :  0.046   0.331   1234
  Planarity :  0.004   0.044   1265
  Dihedral  :  9.705  83.580   1375
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.84 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -2.79 (0.27), residues: 922
  helix: -1.18 (0.25), residues: 427
  sheet: -1.49 (0.62), residues: 70
  loop : -2.62 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 117 
 HIS   0.003   0.001   HIS A 349 
 PHE   0.035   0.002   PHE A 155 
 TYR   0.021   0.001   TYR B 303 
 ARG   0.004   0.000   ARG A 162 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.8786 (t) cc_final: 0.8521 (m)
REVERT: A  264 ASN cc_start: 0.7620 (m-40) cc_final: 0.7344 (m110)
REVERT: A  284 ASN cc_start: 0.8420 (m110) cc_final: 0.8064 (t0)
REVERT: A  350 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6822 (mp)
REVERT: A  398 PHE cc_start: 0.8400 (m-10) cc_final: 0.8039 (m-10)
REVERT: A  471 HIS cc_start: 0.4138 (OUTLIER) cc_final: 0.2772 (m-70)
REVERT: B  146 ARG cc_start: 0.7928 (mmt180) cc_final: 0.7426 (mpt90)
REVERT: B  170 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.6594 (p0)
REVERT: B  258 PHE cc_start: 0.7733 (m-80) cc_final: 0.6720 (m-80)
REVERT: B  262 TRP cc_start: 0.8974 (m-10) cc_final: 0.8357 (m-90)
  outliers start: 35
  outliers final: 29
  residues processed: 148
  average time/residue: 0.1795
  time to fit residues: 37.5025
Evaluate side-chains
  152 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  358 THR
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  493 ASP
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 90 optimal weight:    0.0170
   chunk 83 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0020
   chunk 7 optimal weight:    0.1980
   chunk 55 optimal weight:    0.0050
   chunk 44 optimal weight:    0.4980
   chunk 57 optimal weight:    2.9990
   chunk 76 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0980
   overall best weight:    0.0640

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7583  Z= 0.142
  Angle     :  0.687  15.386  10350  Z= 0.317
  Chirality :  0.045   0.381   1234
  Planarity :  0.003   0.037   1265
  Dihedral  :  9.491  79.420   1375
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 24.61 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

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: -2.66 (0.27), residues: 922
  helix: -1.03 (0.26), residues: 427
  sheet: -1.41 (0.66), residues: 60
  loop : -2.59 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 117 
 HIS   0.002   0.001   HIS A 358 
 PHE   0.037   0.001   PHE A 155 
 TYR   0.015   0.001   TYR B 149 
 ARG   0.008   0.000   ARG A 162 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.8769 (t) cc_final: 0.8523 (m)
REVERT: A  264 ASN cc_start: 0.7513 (m-40) cc_final: 0.7212 (m110)
REVERT: A  350 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6668 (mp)
REVERT: A  398 PHE cc_start: 0.8331 (m-10) cc_final: 0.7988 (m-10)
REVERT: A  469 TRP cc_start: 0.4334 (p-90) cc_final: 0.3591 (p-90)
REVERT: A  471 HIS cc_start: 0.3990 (OUTLIER) cc_final: 0.2700 (m-70)
REVERT: B  170 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6496 (p0)
REVERT: B  258 PHE cc_start: 0.7691 (m-80) cc_final: 0.6681 (m-80)
REVERT: B  262 TRP cc_start: 0.8977 (m-10) cc_final: 0.8384 (m-90)
  outliers start: 30
  outliers final: 22
  residues processed: 147
  average time/residue: 0.1763
  time to fit residues: 35.7846
Evaluate side-chains
  145 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  358 THR
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  493 ASP
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0170
   chunk 20 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.158563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125733 restraints weight = 10167.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.124336 restraints weight = 15527.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.125985 restraints weight = 14590.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7583  Z= 0.192
  Angle     :  0.665   9.665  10350  Z= 0.311
  Chirality :  0.045   0.291   1234
  Planarity :  0.004   0.041   1265
  Dihedral  :  9.400  76.111   1375
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 24.36 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -2.58 (0.27), residues: 922
  helix: -0.99 (0.26), residues: 431
  sheet: -1.47 (0.65), residues: 60
  loop : -2.51 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  79 
 HIS   0.002   0.001   HIS A 349 
 PHE   0.034   0.002   PHE A 155 
 TYR   0.021   0.001   TYR B 303 
 ARG   0.006   0.000   ARG A 162 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1842.73 seconds
wall clock time: 34 minutes 1.93 seconds (2041.93 seconds total)