Starting phenix.real_space_refine
on Thu Jan 18 18:55:10 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/01_2024/8hgo_34744.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/01_2024/8hgo_34744.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/01_2024/8hgo_34744.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/01_2024/8hgo_34744.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/01_2024/8hgo_34744.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/01_2024/8hgo_34744.pdb"
  }
  resolution = 3.31
  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=   0.013
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     109      5.16       5
     C    5714      2.51       5
     N    1636      2.21       5
     O    1768      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B ARG   98": "NH1" <-> "NH2"
    Residue "B ARG  100": "NH1" <-> "NH2"
    Residue "B ARG  138": "NH1" <-> "NH2"
    Residue "B ARG  188": "NH1" <-> "NH2"
    Residue "B ARG  351": "NH1" <-> "NH2"
    Residue "B ARG  552": "NH1" <-> "NH2"
    Residue "B ARG  558": "NH1" <-> "NH2"
    Residue "A ARG  255": "NH1" <-> "NH2"
    Residue "A ARG  377": "NH1" <-> "NH2"
    Residue "A ARG  414": "NH1" <-> "NH2"
    Residue "A PHE  481": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  531": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib"
  Total number of atoms: 9227
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 4345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4345
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 35, 'TRANS': 527}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 568, 4391
          Classifications: {'peptide': 568}
          Link IDs: {'PTRANS': 26, 'TRANS': 541}
    Chain: "C"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 385
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "D"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 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
  Residues with excluded nonbonded symmetry interactions: 9
    residue:
      pdb=" N   ASN A 182 " occ=0.00
      ... (6 atoms not shown)
      pdb=" ND2 ASN A 182 " occ=0.00
    residue:
      pdb=" N   HIS A 183 " occ=0.00
      ... (8 atoms not shown)
      pdb=" NE2 HIS A 183 " occ=0.00
    residue:
      pdb=" N   LEU A 184 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 184 " occ=0.00
    residue:
      pdb=" N   GLY A 203 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A 203 " occ=0.00
    residue:
      pdb=" N   CYS A 329 " occ=0.00
      ... (4 atoms not shown)
      pdb=" SG  CYS A 329 " occ=0.00
    residue:
      pdb=" N   GLU A 330 " occ=0.00
      ... (7 atoms not shown)
      pdb=" OE2 GLU A 330 " occ=0.00
    residue:
      pdb=" N   GLY A 331 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A 331 " occ=0.00
    residue:
      pdb=" N   PRO A 332 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CD  PRO A 332 " occ=0.00
    residue:
      pdb=" N   CYS A 333 " occ=0.00
      ... (4 atoms not shown)
      pdb=" SG  CYS A 333 " occ=0.00
  Time building chain proxies: 5.39, per 1000 atoms: 0.58
  Number of scatterers: 9227
  At special positions: 0
  Unit cell: (78.11, 131.61, 126.26, 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     109     16.00
     O    1768      8.00
     N    1636      7.00
     C    5714      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=47, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  26 " - pdb=" SG  CYS B  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 195 " - pdb=" SG  CYS B 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 199 " - pdb=" SG  CYS B 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 220 " - pdb=" SG  CYS B 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 224 " - pdb=" SG  CYS B 235 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 236 " - pdb=" SG  CYS B 244 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 240 " - pdb=" SG  CYS B 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 255 " - pdb=" SG  CYS B 264 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 268 " - pdb=" SG  CYS B 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 299 " - pdb=" SG  CYS B 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 315 " - pdb=" SG  CYS B 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 334 " - pdb=" SG  CYS B 338 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 342 " - pdb=" SG  CYS B 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 475 " - pdb=" SG  CYS B 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 511 " - pdb=" SG  CYS B 520 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 515 " - pdb=" SG  CYS B 528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 531 " - pdb=" SG  CYS B 540 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 544 " - pdb=" SG  CYS B 560 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 563 " - pdb=" SG  CYS B 576 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 567 " - pdb=" SG  CYS B 584 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 587 " - pdb=" SG  CYS B 596 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 157 " - pdb=" SG  CYS A 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 190 " - pdb=" SG  CYS A 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 194 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 215 " - pdb=" SG  CYS A 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 219 " - pdb=" SG  CYS A 231 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 240 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 251 " - pdb=" SG  CYS A 260 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 264 " - pdb=" SG  CYS A 291 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 295 " - pdb=" SG  CYS A 307 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 311 " - pdb=" SG  CYS A 326 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 329 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 337 " - pdb=" SG  CYS A 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 470 " - pdb=" SG  CYS A 499 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 506 " - pdb=" SG  CYS A 515 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 510 " - pdb=" SG  CYS A 523 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 526 " - pdb=" SG  CYS A 535 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 539 " - pdb=" SG  CYS A 555 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 558 " - pdb=" SG  CYS A 571 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 562 " - pdb=" SG  CYS A 579 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 582 " - pdb=" SG  CYS A 591 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C  20 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  14 " - pdb=" SG  CYS C  31 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  33 " - pdb=" SG  CYS C  42 " 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=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
    BETA1-3
      " NAG D   2 " - " BMA D   3 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A 801 " - " ASN A  56 "
      " NAG A 802 " - " ASN A 175 "
      " NAG D   1 " - " ASN A 352 "
      " NAG E   1 " - " ASN B 259 "
  Time building additional restraints: 3.88
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2174

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 21 sheets defined
      11.9% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 41 through 51
      removed outlier: 3.825A  pdb=" N   GLN B  51 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 75
      removed outlier: 3.965A  pdb=" N   GLN B  75 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 173
      removed outlier: 4.076A  pdb=" N   ILE B 172 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 212
      removed outlier: 3.566A  pdb=" N   ASP B 211 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   CYS B 212 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 208 through 212'
    Processing helix  chain 'B' and resid 361 through 365
      removed outlier: 3.534A  pdb=" N   PHE B 364 " --> pdb=" O   ILE B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 401
      removed outlier: 3.865A  pdb=" N   VAL B 399 " --> pdb=" O   GLN B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 426
      removed outlier: 3.601A  pdb=" N   GLN B 426 " --> pdb=" O   SER B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 440
    Processing helix  chain 'B' and resid 501 through 506
      removed outlier: 4.063A  pdb=" N   GLY B 506 " --> pdb=" O   ASP B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 519
      removed outlier: 3.787A  pdb=" N   GLY B 518 " --> pdb=" O   CYS B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 584
      removed outlier: 3.586A  pdb=" N   GLN B 583 " --> pdb=" O   GLU B 580 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   CYS B 584 " --> pdb=" O   ALA B 581 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 580 through 584'
    Processing helix  chain 'A' and resid 43 through 55
    Processing helix  chain 'A' and resid 76 through 82
      removed outlier: 3.798A  pdb=" N   THR A  81 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ILE A  82 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 198
      removed outlier: 3.746A  pdb=" N   GLY A 197 " --> pdb=" O   CYS A 194 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER A 198 " --> pdb=" O   PRO A 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 194 through 198'
    Processing helix  chain 'A' and resid 342 through 346
      removed outlier: 3.793A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS A 346 " --> pdb=" O   GLY A 343 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 342 through 346'
    Processing helix  chain 'A' and resid 355 through 360
      removed outlier: 3.934A  pdb=" N   LYS A 360 " --> pdb=" O   LYS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 378
    Processing helix  chain 'A' and resid 388 through 397
      removed outlier: 3.573A  pdb=" N   LEU A 392 " --> pdb=" O   PRO A 389 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASP A 393 " --> pdb=" O   GLN A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 421
      removed outlier: 3.888A  pdb=" N   PHE A 420 " --> pdb=" O   LEU A 417 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLU A 421 " --> pdb=" O   HIS A 418 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 417 through 421'
    Processing helix  chain 'A' and resid 431 through 434
    Processing helix  chain 'A' and resid 476 through 480
      removed outlier: 3.516A  pdb=" N   LYS A 479 " --> pdb=" O   ASN A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 523
      removed outlier: 4.427A  pdb=" N   CYS A 523 " --> pdb=" O   PRO A 520 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 11
    Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26
      removed outlier: 3.743A  pdb=" N   CYS B  26 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63
      removed outlier: 6.411A  pdb=" N   LEU B  60 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   ALA B  87 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LEU B  62 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU B 114 " --> pdb=" O   LEU B 154 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL B 116 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 258 through 260
    Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 275
    Processing sheet with id=AA5, first strand: chain 'B' and resid 289 through 291
    Processing sheet with id=AA6, first strand: chain 'B' and resid 319 through 320
      removed outlier: 3.695A  pdb=" N   GLU B 332 " --> pdb=" O   GLN B 320 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 370
    Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 376
      removed outlier: 6.440A  pdb=" N   LEU B 374 " --> pdb=" O   TYR B 411 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   HIS B 469 " --> pdb=" O   LEU B 445 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ALA B 466 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   THR B 496 " --> pdb=" O   ALA B 466 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ILE B 468 " --> pdb=" O   THR B 496 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 553 through 555
    Processing sheet with id=AB1, first strand: chain 'A' and resid 30 through 31
    Processing sheet with id=AB2, first strand: chain 'A' and resid 40 through 41
      removed outlier: 6.976A  pdb=" N   GLN A  40 " --> pdb=" O   CYS C  33 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 65 through 68
      removed outlier: 6.670A  pdb=" N   LEU A  65 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   ALA A  92 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ILE A  67 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   VAL A  89 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   LEU A 122 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ILE A  91 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU A 119 " --> pdb=" O   ARG A 149 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   SER A 151 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL A 121 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 236 through 240
      removed outlier: 3.574A  pdb=" N   ALA A 237 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   VAL A 250 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
      removed outlier: 8.821A  pdb=" N   GLY A 239 " --> pdb=" O   CYS A 248 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   CYS A 248 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'A' and resid 254 through 256
      removed outlier: 3.564A  pdb=" N   PHE A 254 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS A 261 " --> pdb=" O   PHE A 254 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 300 through 301
    Processing sheet with id=AB7, first strand: chain 'A' and resid 316 through 317
    Processing sheet with id=AB8, first strand: chain 'A' and resid 364 through 365
    Processing sheet with id=AB9, first strand: chain 'A' and resid 369 through 371
      removed outlier: 6.569A  pdb=" N   LEU A 369 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   LEU A 405 " --> pdb=" O   ALA A 439 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ILE A 462 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   ALA A 439 " --> pdb=" O   ILE A 462 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL A 461 " --> pdb=" O   LYS A 489 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 548 through 549
      removed outlier: 3.600A  pdb=" N   PHE A 549 " --> pdb=" O   ILE A 556 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 556 " --> pdb=" O   PHE A 549 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'A' and resid 585 through 587
    Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 38

    97 hydrogen bonds defined for protein.
    186 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: 2.61

  Time building geometry restraints manager: 4.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3127
        1.34 -     1.46: 2001
        1.46 -     1.58: 4168
        1.58 -     1.70: 0
        1.70 -     1.82: 124
  Bond restraints: 9420
  Sorted by residual:
  bond pdb=" C5  MAN D   4 "
       pdb=" O5  MAN D   4 "
    ideal  model  delta    sigma   weight residual
    1.418  1.473 -0.055 2.00e-02 2.50e+03 7.67e+00
  bond pdb=" C   PRO B 593 "
       pdb=" N   PRO B 594 "
    ideal  model  delta    sigma   weight residual
    1.334  1.394 -0.060 2.34e-02 1.83e+03 6.51e+00
  bond pdb=" C   LYS B 336 "
       pdb=" N   PRO B 337 "
    ideal  model  delta    sigma   weight residual
    1.334  1.392 -0.058 2.34e-02 1.83e+03 6.17e+00
  bond pdb=" C5  BMA D   3 "
       pdb=" O5  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.462 -0.045 2.00e-02 2.50e+03 5.15e+00
  bond pdb=" C1  MAN D   4 "
       pdb=" O5  MAN D   4 "
    ideal  model  delta    sigma   weight residual
    1.399  1.443 -0.044 2.00e-02 2.50e+03 4.86e+00
  ... (remaining 9415 not shown)

  Histogram of bond angle deviations from ideal:
      100.45 -   107.16: 369
      107.16 -   113.87: 5176
      113.87 -   120.58: 3500
      120.58 -   127.29: 3628
      127.29 -   134.00: 96
  Bond angle restraints: 12769
  Sorted by residual:
  angle pdb=" N   LEU A 509 "
        pdb=" CA  LEU A 509 "
        pdb=" C   LEU A 509 "
      ideal   model   delta    sigma   weight residual
     110.80  121.59  -10.79 2.13e+00 2.20e-01 2.57e+01
  angle pdb=" N   ARG A 334 "
        pdb=" CA  ARG A 334 "
        pdb=" C   ARG A 334 "
      ideal   model   delta    sigma   weight residual
     110.97  115.32   -4.35 1.09e+00 8.42e-01 1.59e+01
  angle pdb=" C   ALA B 324 "
        pdb=" N   GLU B 325 "
        pdb=" CA  GLU B 325 "
      ideal   model   delta    sigma   weight residual
     122.08  127.78   -5.70 1.47e+00 4.63e-01 1.50e+01
  angle pdb=" C   GLU A 204 "
        pdb=" N   GLU A 205 "
        pdb=" CA  GLU A 205 "
      ideal   model   delta    sigma   weight residual
     121.54  128.81   -7.27 1.91e+00 2.74e-01 1.45e+01
  angle pdb=" N   PRO B 593 "
        pdb=" CA  PRO B 593 "
        pdb=" C   PRO B 593 "
      ideal   model   delta    sigma   weight residual
     110.70  114.91   -4.21 1.22e+00 6.72e-01 1.19e+01
  ... (remaining 12764 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.75: 5706
       20.75 -    41.50: 145
       41.50 -    62.25: 40
       62.25 -    83.00: 20
       83.00 -   103.75: 6
  Dihedral angle restraints: 5917
    sinusoidal: 2535
      harmonic: 3382
  Sorted by residual:
  dihedral pdb=" CB  CYS B 299 "
           pdb=" SG  CYS B 299 "
           pdb=" SG  CYS B 311 "
           pdb=" CB  CYS B 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -176.55  -90.45     1      1.00e+01 1.00e-02 9.67e+01
  dihedral pdb=" CB  CYS A 219 "
           pdb=" SG  CYS A 219 "
           pdb=" SG  CYS A 231 "
           pdb=" CB  CYS A 231 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.51  -87.49     1      1.00e+01 1.00e-02 9.18e+01
  dihedral pdb=" CB  CYS A 190 "
           pdb=" SG  CYS A 190 "
           pdb=" SG  CYS A 199 "
           pdb=" CB  CYS A 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -168.44   82.44     1      1.00e+01 1.00e-02 8.34e+01
  ... (remaining 5914 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1224
       0.076 -    0.152: 190
       0.152 -    0.228: 6
       0.228 -    0.304: 2
       0.304 -    0.380: 3
  Chirality restraints: 1425
  Sorted by residual:
  chirality pdb=" C2  NAG A 802 "
            pdb=" C1  NAG A 802 "
            pdb=" C3  NAG A 802 "
            pdb=" N2  NAG A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.11   -0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" CA  LEU A 509 "
            pdb=" N   LEU A 509 "
            pdb=" C   LEU A 509 "
            pdb=" CB  LEU A 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" C1  NAG A 802 "
            pdb=" ND2 ASN A 175 "
            pdb=" C2  NAG A 802 "
            pdb=" O5  NAG A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.55e+00
  ... (remaining 1422 not shown)

  Planarity restraints: 1683
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 519 "    0.035 5.00e-02 4.00e+02   5.27e-02 4.44e+00
        pdb=" N   PRO A 520 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 520 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 520 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 511 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.25e+00
        pdb=" N   PRO A 512 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 512 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 512 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 372 "   -0.033 5.00e-02 4.00e+02   5.00e-02 3.99e+00
        pdb=" N   PRO A 373 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 373 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 373 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1680 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2411
        2.81 -     3.33: 7501
        3.33 -     3.85: 14605
        3.85 -     4.38: 16494
        4.38 -     4.90: 28622
  Nonbonded interactions: 69633
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 163 "
            pdb=" O   HIS B 193 "
     model   vdw
     2.284 2.440
  nonbonded pdb=" ND1 HIS A 507 "
            pdb=" O   ALA A 508 "
     model   vdw
     2.315 2.520
  nonbonded pdb=" OG  SER B  38 "
            pdb=" OG1 THR B  41 "
     model   vdw
     2.324 2.440
  nonbonded pdb=" OE2 GLU A  66 "
            pdb=" OH  TYR A  88 "
     model   vdw
     2.349 2.440
  nonbonded pdb=" O   VAL B 356 "
            pdb=" OG  SER B 380 "
     model   vdw
     2.365 2.440
  ... (remaining 69628 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.870
  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:          12.020
  Check model and map are aligned:         0.160
  Set scattering table:                    0.100
  Process input model:                     28.640
  Find NCS groups from input model:        0.300
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6544
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      :  0.004   0.060   9420  Z= 0.239
  Angle     :  0.711  10.795  12769  Z= 0.397
  Chirality :  0.054   0.380   1425
  Planarity :  0.007   0.053   1679
  Dihedral  :  9.525 103.750   3602
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.03 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  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: -3.74 (0.20), residues: 1170
  helix: -3.97 (0.38), residues: 41
  sheet: -2.80 (0.49), residues: 91
  loop : -2.68 (0.16), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 452 
 HIS   0.015   0.001   HIS B  48 
 PHE   0.019   0.002   PHE A 404 
 TYR   0.014   0.001   TYR B 554 
 ARG   0.004   0.000   ARG B 536 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.7294 (t70) cc_final: 0.6925 (t70)
REVERT: B   89 ASN cc_start: 0.7573 (m-40) cc_final: 0.7250 (m110)
REVERT: B  103 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7373 (mtp85)
REVERT: B  112 TYR cc_start: 0.6756 (m-80) cc_final: 0.6533 (m-80)
REVERT: B  164 GLN cc_start: 0.6589 (pm20) cc_final: 0.6193 (pm20)
REVERT: B  183 LEU cc_start: 0.8231 (mp) cc_final: 0.7844 (tp)
REVERT: B  228 LYS cc_start: 0.7510 (mtpt) cc_final: 0.7278 (mtpt)
REVERT: B  405 GLU cc_start: 0.6892 (tt0) cc_final: 0.6636 (tt0)
REVERT: B  434 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7945 (mtt180)
REVERT: B  460 GLU cc_start: 0.6684 (tt0) cc_final: 0.6187 (tt0)
REVERT: B  467 LEU cc_start: 0.8448 (tp) cc_final: 0.7783 (tp)
REVERT: B  541 VAL cc_start: 0.7565 (m) cc_final: 0.7159 (p)
REVERT: B  561 LEU cc_start: 0.7389 (mt) cc_final: 0.7124 (mt)
REVERT: A   45 GLU cc_start: 0.7186 (mp0) cc_final: 0.6738 (mp0)
REVERT: A   46 ASP cc_start: 0.7642 (t70) cc_final: 0.7218 (t0)
REVERT: A  152 ASN cc_start: 0.7274 (m110) cc_final: 0.6942 (m110)
REVERT: A  160 GLU cc_start: 0.7180 (pm20) cc_final: 0.6471 (pm20)
REVERT: A  234 ASN cc_start: 0.7890 (t0) cc_final: 0.7649 (t0)
REVERT: A  268 MET cc_start: 0.5860 (mtm) cc_final: 0.5359 (mtm)
REVERT: A  277 MET cc_start: 0.5040 (mtt) cc_final: 0.4820 (mtt)
REVERT: A  292 VAL cc_start: 0.7916 (m) cc_final: 0.7545 (p)
REVERT: A  293 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7713 (mtpp)
REVERT: A  294 LYS cc_start: 0.7981 (tttt) cc_final: 0.7751 (tttt)
REVERT: A  325 LYS cc_start: 0.7243 (mttt) cc_final: 0.6891 (mtmm)
REVERT: A  360 LYS cc_start: 0.7592 (tttt) cc_final: 0.7361 (tttt)
REVERT: A  425 ILE cc_start: 0.8526 (tt) cc_final: 0.7990 (tt)
REVERT: A  430 THR cc_start: 0.7999 (m) cc_final: 0.7331 (p)
REVERT: A  431 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7855 (mtmm)
REVERT: A  593 LYS cc_start: 0.6587 (tptp) cc_final: 0.6324 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.2822
  time to fit residues: 105.4842
Evaluate side-chains
  231 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.4980
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0020
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 90 optimal weight:    0.0970
   chunk 35 optimal weight:    0.0980
   chunk 55 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0980
   chunk 105 optimal weight:    0.0970
   overall best weight:    0.0784

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

Flipped N/Q/H residues before XYZ refinement:
B  81 GLN
B 302 ASN
B 438 ASN
A  47 HIS
A  64 ASN
** A  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 103 ASN
A 110 ASN
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 206 ASN
A 233 HIS
A 235 GLN
A 486 GLN
** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 552 ASN
A 559 HIS
A 565 GLN
A 584 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6642
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9420  Z= 0.161
  Angle     :  0.617   9.828  12769  Z= 0.310
  Chirality :  0.046   0.247   1425
  Planarity :  0.005   0.042   1679
  Dihedral  :  7.914  62.380   1414
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.41 %
    Favored  : 91.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -3.31 (0.22), residues: 1170
  helix: -3.32 (0.51), residues: 63
  sheet: -2.57 (0.51), residues: 89
  loop : -2.33 (0.18), residues: 1018

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 452 
 HIS   0.005   0.001   HIS A 233 
 PHE   0.024   0.001   PHE A 549 
 TYR   0.019   0.001   TYR B  64 
 ARG   0.012   0.001   ARG B 499 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 260
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.7292 (t70) cc_final: 0.6880 (t70)
REVERT: B   93 GLN cc_start: 0.6925 (pp30) cc_final: 0.6638 (pp30)
REVERT: B  147 GLU cc_start: 0.6693 (tp30) cc_final: 0.6395 (tp30)
REVERT: B  156 GLN cc_start: 0.7572 (mt0) cc_final: 0.7185 (mt0)
REVERT: B  183 LEU cc_start: 0.8292 (mp) cc_final: 0.7930 (tp)
REVERT: B  228 LYS cc_start: 0.7539 (mtpt) cc_final: 0.7198 (mtpt)
REVERT: B  403 LEU cc_start: 0.6683 (tp) cc_final: 0.6349 (tp)
REVERT: B  405 GLU cc_start: 0.6959 (tt0) cc_final: 0.6758 (tt0)
REVERT: B  430 VAL cc_start: 0.8462 (p) cc_final: 0.8240 (t)
REVERT: B  438 ASN cc_start: 0.7409 (m-40) cc_final: 0.7110 (m110)
REVERT: B  561 LEU cc_start: 0.7357 (mt) cc_final: 0.7079 (mt)
REVERT: A   45 GLU cc_start: 0.7247 (mp0) cc_final: 0.6804 (mp0)
REVERT: A   46 ASP cc_start: 0.7688 (t70) cc_final: 0.7327 (t0)
REVERT: A   80 LYS cc_start: 0.8354 (mttp) cc_final: 0.8093 (mttp)
REVERT: A   98 ARG cc_start: 0.7884 (mtp-110) cc_final: 0.7557 (mtp180)
REVERT: A  137 MET cc_start: 0.8420 (mtp) cc_final: 0.8185 (mtp)
REVERT: A  152 ASN cc_start: 0.7309 (m110) cc_final: 0.6936 (m110)
REVERT: A  198 SER cc_start: 0.8058 (m) cc_final: 0.7401 (p)
REVERT: A  254 PHE cc_start: 0.7703 (m-10) cc_final: 0.7445 (m-10)
REVERT: A  255 ARG cc_start: 0.6314 (ttt-90) cc_final: 0.5894 (tmt-80)
REVERT: A  268 MET cc_start: 0.5729 (mtm) cc_final: 0.5236 (mtm)
REVERT: A  277 MET cc_start: 0.5050 (mtt) cc_final: 0.4796 (mtt)
REVERT: A  292 VAL cc_start: 0.7989 (m) cc_final: 0.7470 (p)
REVERT: A  294 LYS cc_start: 0.8018 (tttt) cc_final: 0.7786 (tttt)
REVERT: A  325 LYS cc_start: 0.7213 (mttt) cc_final: 0.6828 (mtmt)
REVERT: A  347 ASP cc_start: 0.6346 (t0) cc_final: 0.5861 (t0)
REVERT: A  430 THR cc_start: 0.8025 (m) cc_final: 0.7370 (p)
REVERT: A  480 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7706 (tt)
REVERT: A  578 ASN cc_start: 0.6526 (m-40) cc_final: 0.6259 (m-40)
REVERT: A  593 LYS cc_start: 0.6521 (tptp) cc_final: 0.6299 (tptp)
REVERT: C   38 ILE cc_start: 0.8312 (tt) cc_final: 0.7967 (pt)
  outliers start: 13
  outliers final: 8
  residues processed: 262
  average time/residue: 0.2498
  time to fit residues: 86.5301
Evaluate side-chains
  252 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 243
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  329 GLN
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  327 LYS
Chi-restraints excluded: chain A residue  480 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0470
   chunk 71 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 105 optimal weight:    0.2980
   chunk 114 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 84 optimal weight:    0.0670
   overall best weight:    0.3216

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

Flipped N/Q/H residues before XYZ refinement:
B  42 HIS
B  81 GLN
** B  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 559 HIS
A 158 ASN
A 233 HIS
A 493 ASN
A 552 ASN
C  16 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9420  Z= 0.225
  Angle     :  0.618   9.748  12769  Z= 0.316
  Chirality :  0.049   0.304   1425
  Planarity :  0.005   0.043   1679
  Dihedral  :  7.118  56.408   1414
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  :  9.07 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -3.00 (0.22), residues: 1170
  helix: -3.23 (0.50), residues: 75
  sheet: -2.24 (0.51), residues: 92
  loop : -2.07 (0.18), residues: 1003

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  49 
 HIS   0.006   0.001   HIS A 233 
 PHE   0.018   0.002   PHE A 549 
 TYR   0.018   0.002   TYR B  64 
 ARG   0.011   0.001   ARG A 252 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 265
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   27 THR cc_start: 0.7907 (m) cc_final: 0.7683 (m)
REVERT: B   30 ASP cc_start: 0.7470 (t70) cc_final: 0.6803 (t70)
REVERT: B   93 GLN cc_start: 0.6954 (pp30) cc_final: 0.6624 (pp30)
REVERT: B  109 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6373 (mm-30)
REVERT: B  112 TYR cc_start: 0.6965 (m-80) cc_final: 0.6542 (m-80)
REVERT: B  147 GLU cc_start: 0.6777 (tp30) cc_final: 0.6440 (tp30)
REVERT: B  156 GLN cc_start: 0.7757 (mt0) cc_final: 0.7414 (mt0)
REVERT: B  164 GLN cc_start: 0.6847 (pm20) cc_final: 0.6392 (pm20)
REVERT: B  183 LEU cc_start: 0.8279 (mp) cc_final: 0.7774 (tp)
REVERT: B  228 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7327 (mtmm)
REVERT: B  274 TYR cc_start: 0.7869 (t80) cc_final: 0.7548 (t80)
REVERT: B  284 ASN cc_start: 0.7332 (t0) cc_final: 0.6982 (t0)
REVERT: B  403 LEU cc_start: 0.6958 (tp) cc_final: 0.6710 (tp)
REVERT: B  405 GLU cc_start: 0.6964 (tt0) cc_final: 0.6732 (tt0)
REVERT: B  460 GLU cc_start: 0.6875 (tt0) cc_final: 0.6640 (tp30)
REVERT: B  538 GLN cc_start: 0.6431 (pp30) cc_final: 0.6153 (pm20)
REVERT: B  568 GLN cc_start: 0.6592 (tm-30) cc_final: 0.6182 (tm-30)
REVERT: A   45 GLU cc_start: 0.7236 (mp0) cc_final: 0.6875 (mp0)
REVERT: A   46 ASP cc_start: 0.7822 (t70) cc_final: 0.7453 (t0)
REVERT: A   67 ILE cc_start: 0.8313 (mt) cc_final: 0.8103 (mt)
REVERT: A   98 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7710 (mtp180)
REVERT: A  137 MET cc_start: 0.8435 (mtp) cc_final: 0.8179 (mtp)
REVERT: A  198 SER cc_start: 0.8191 (m) cc_final: 0.7537 (p)
REVERT: A  252 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7213 (mtp85)
REVERT: A  255 ARG cc_start: 0.6378 (ttt-90) cc_final: 0.6122 (tmt-80)
REVERT: A  256 ASP cc_start: 0.7323 (t70) cc_final: 0.6926 (t70)
REVERT: A  268 MET cc_start: 0.5846 (mtm) cc_final: 0.5383 (mtm)
REVERT: A  277 MET cc_start: 0.5246 (mtt) cc_final: 0.4926 (mtt)
REVERT: A  292 VAL cc_start: 0.8118 (m) cc_final: 0.7716 (p)
REVERT: A  294 LYS cc_start: 0.8094 (tttt) cc_final: 0.7844 (tttt)
REVERT: A  316 TYR cc_start: 0.6509 (t80) cc_final: 0.6035 (t80)
REVERT: A  325 LYS cc_start: 0.7328 (mttt) cc_final: 0.6866 (mtmt)
REVERT: A  347 ASP cc_start: 0.6571 (t0) cc_final: 0.6114 (t0)
REVERT: A  391 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7041 (mm-30)
REVERT: A  430 THR cc_start: 0.8060 (m) cc_final: 0.7403 (p)
REVERT: A  479 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7330 (pttm)
REVERT: A  489 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7332 (ttmm)
REVERT: A  551 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6512 (tm-30)
REVERT: A  578 ASN cc_start: 0.6791 (m-40) cc_final: 0.6474 (m-40)
REVERT: A  593 LYS cc_start: 0.6560 (tptp) cc_final: 0.6332 (tptp)
REVERT: C   38 ILE cc_start: 0.8378 (tt) cc_final: 0.8036 (pt)
  outliers start: 28
  outliers final: 18
  residues processed: 273
  average time/residue: 0.2507
  time to fit residues: 90.2112
Evaluate side-chains
  250 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 231
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  227 CYS
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  329 GLN
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  251 CYS
Chi-restraints excluded: chain A residue  261 LYS
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  515 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 105 optimal weight:    0.6980
   chunk 112 optimal weight:    0.4980
   chunk 55 optimal weight:    0.7980
   chunk 100 optimal weight:    0.5980
   chunk 30 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 260 HIS
B 446 GLN
B 470 HIS
A 552 ASN
** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.109   9420  Z= 0.361
  Angle     :  0.704  13.226  12769  Z= 0.356
  Chirality :  0.053   0.454   1425
  Planarity :  0.005   0.047   1679
  Dihedral  :  7.138  58.804   1414
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 10.15 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.80 (0.22), residues: 1170
  helix: -2.99 (0.56), residues: 59
  sheet: -2.24 (0.53), residues: 82
  loop : -1.96 (0.18), residues: 1029

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  49 
 HIS   0.006   0.001   HIS B 260 
 PHE   0.032   0.002   PHE A 549 
 TYR   0.019   0.002   TYR B 163 
 ARG   0.007   0.001   ARG B 459 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 261
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: B   27 THR cc_start: 0.7805 (m) cc_final: 0.7593 (m)
REVERT: B   30 ASP cc_start: 0.7604 (t70) cc_final: 0.6958 (t70)
REVERT: B   75 GLN cc_start: 0.7615 (pt0) cc_final: 0.7364 (pt0)
REVERT: B  112 TYR cc_start: 0.7235 (m-80) cc_final: 0.6878 (m-80)
REVERT: B  147 GLU cc_start: 0.6756 (tp30) cc_final: 0.6346 (tp30)
REVERT: B  228 LYS cc_start: 0.7735 (mtpt) cc_final: 0.7462 (mtmm)
REVERT: B  274 TYR cc_start: 0.7834 (t80) cc_final: 0.7543 (t80)
REVERT: B  284 ASN cc_start: 0.7803 (t0) cc_final: 0.7469 (t0)
REVERT: B  421 ASP cc_start: 0.6727 (p0) cc_final: 0.6427 (p0)
REVERT: B  452 TRP cc_start: 0.8005 (p90) cc_final: 0.7801 (p90)
REVERT: B  460 GLU cc_start: 0.6861 (tt0) cc_final: 0.6547 (tp30)
REVERT: B  538 GLN cc_start: 0.6521 (OUTLIER) cc_final: 0.6200 (pm20)
REVERT: A   45 GLU cc_start: 0.7279 (mp0) cc_final: 0.7044 (mp0)
REVERT: A   46 ASP cc_start: 0.7749 (t70) cc_final: 0.7305 (t0)
REVERT: A   97 GLU cc_start: 0.6579 (mp0) cc_final: 0.6152 (mp0)
REVERT: A  133 LYS cc_start: 0.7111 (mttt) cc_final: 0.6770 (mmmm)
REVERT: A  142 GLU cc_start: 0.6866 (tt0) cc_final: 0.6619 (tt0)
REVERT: A  148 VAL cc_start: 0.8350 (t) cc_final: 0.7978 (m)
REVERT: A  198 SER cc_start: 0.8269 (m) cc_final: 0.7560 (p)
REVERT: A  268 MET cc_start: 0.6093 (mtm) cc_final: 0.5605 (mtm)
REVERT: A  277 MET cc_start: 0.5506 (mtt) cc_final: 0.5185 (mtt)
REVERT: A  292 VAL cc_start: 0.8135 (m) cc_final: 0.7834 (p)
REVERT: A  316 TYR cc_start: 0.6557 (t80) cc_final: 0.6238 (t80)
REVERT: A  325 LYS cc_start: 0.7466 (mttt) cc_final: 0.6973 (mtmt)
REVERT: A  347 ASP cc_start: 0.6681 (t0) cc_final: 0.6220 (t0)
REVERT: A  360 LYS cc_start: 0.7996 (tttt) cc_final: 0.7717 (ttmm)
REVERT: A  391 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7227 (mm-30)
REVERT: A  430 THR cc_start: 0.8099 (m) cc_final: 0.7482 (p)
REVERT: A  431 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7758 (mtmt)
REVERT: A  479 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7508 (pttt)
REVERT: A  487 LYS cc_start: 0.7060 (mtmm) cc_final: 0.6749 (mtmm)
REVERT: A  584 HIS cc_start: 0.6041 (m90) cc_final: 0.5754 (m170)
REVERT: A  593 LYS cc_start: 0.6678 (tptp) cc_final: 0.6119 (tptp)
  outliers start: 31
  outliers final: 23
  residues processed: 272
  average time/residue: 0.2398
  time to fit residues: 86.9738
Evaluate side-chains
  271 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 246
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  329 GLN
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  538 GLN
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  251 CYS
Chi-restraints excluded: chain A residue  293 LYS
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  515 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 93 optimal weight:    0.2980
   chunk 63 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0980
   chunk 77 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0970
   overall best weight:    0.3378

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

Flipped N/Q/H residues before XYZ refinement:
B 527 GLN
A 163 GLN
A 552 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.4423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9420  Z= 0.239
  Angle     :  0.623   9.775  12769  Z= 0.318
  Chirality :  0.049   0.467   1425
  Planarity :  0.004   0.043   1679
  Dihedral  :  6.723  57.612   1414
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 11.80 %
    Favored  : 85.07 %
  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: -2.69 (0.22), residues: 1170
  helix: -2.81 (0.58), residues: 59
  sheet: -2.45 (0.48), residues: 94
  loop : -1.84 (0.18), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  49 
 HIS   0.005   0.001   HIS A 507 
 PHE   0.032   0.002   PHE A 549 
 TYR   0.014   0.001   TYR B  83 
 ARG   0.008   0.001   ARG B  47 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 249
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.7545 (t70) cc_final: 0.6906 (t70)
REVERT: B   49 LEU cc_start: 0.8023 (tt) cc_final: 0.7810 (tp)
REVERT: B   75 GLN cc_start: 0.7603 (pt0) cc_final: 0.7364 (pt0)
REVERT: B  112 TYR cc_start: 0.7145 (m-80) cc_final: 0.6804 (m-80)
REVERT: B  138 ARG cc_start: 0.6666 (mmm160) cc_final: 0.6399 (mmm160)
REVERT: B  147 GLU cc_start: 0.6756 (tp30) cc_final: 0.6353 (tp30)
REVERT: B  156 GLN cc_start: 0.7703 (mt0) cc_final: 0.7493 (mt0)
REVERT: B  164 GLN cc_start: 0.7585 (pm20) cc_final: 0.6949 (pm20)
REVERT: B  183 LEU cc_start: 0.8189 (mp) cc_final: 0.7770 (tp)
REVERT: B  188 ARG cc_start: 0.7082 (mmt-90) cc_final: 0.6861 (mmt-90)
REVERT: B  211 ASP cc_start: 0.7294 (t0) cc_final: 0.7091 (t0)
REVERT: B  228 LYS cc_start: 0.7760 (mtpt) cc_final: 0.7464 (mtmm)
REVERT: B  261 SER cc_start: 0.7744 (m) cc_final: 0.7408 (p)
REVERT: B  274 TYR cc_start: 0.7831 (t80) cc_final: 0.7485 (t80)
REVERT: B  284 ASN cc_start: 0.7737 (t0) cc_final: 0.7404 (t0)
REVERT: B  421 ASP cc_start: 0.6526 (p0) cc_final: 0.6232 (p0)
REVERT: B  538 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.6248 (pm20)
REVERT: B  568 GLN cc_start: 0.6810 (tm-30) cc_final: 0.6346 (tm-30)
REVERT: A   45 GLU cc_start: 0.7252 (mp0) cc_final: 0.6944 (mp0)
REVERT: A   46 ASP cc_start: 0.7709 (t70) cc_final: 0.7240 (t0)
REVERT: A   67 ILE cc_start: 0.8241 (mt) cc_final: 0.8037 (mt)
REVERT: A   98 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7737 (mtp180)
REVERT: A  125 TYR cc_start: 0.7885 (p90) cc_final: 0.7323 (p90)
REVERT: A  133 LYS cc_start: 0.7085 (mttt) cc_final: 0.6672 (mmmm)
REVERT: A  142 GLU cc_start: 0.6914 (tt0) cc_final: 0.6641 (tt0)
REVERT: A  148 VAL cc_start: 0.8355 (t) cc_final: 0.7985 (m)
REVERT: A  160 GLU cc_start: 0.7669 (pm20) cc_final: 0.7319 (pm20)
REVERT: A  198 SER cc_start: 0.8288 (m) cc_final: 0.7601 (p)
REVERT: A  263 THR cc_start: 0.8007 (m) cc_final: 0.7665 (p)
REVERT: A  268 MET cc_start: 0.6082 (mtm) cc_final: 0.5572 (mtm)
REVERT: A  277 MET cc_start: 0.5511 (mtt) cc_final: 0.5164 (mtt)
REVERT: A  292 VAL cc_start: 0.8106 (m) cc_final: 0.7810 (p)
REVERT: A  325 LYS cc_start: 0.7015 (mttt) cc_final: 0.6511 (mtmm)
REVERT: A  327 LYS cc_start: 0.7636 (ptpp) cc_final: 0.7270 (pttm)
REVERT: A  347 ASP cc_start: 0.6731 (t0) cc_final: 0.6261 (t0)
REVERT: A  360 LYS cc_start: 0.8012 (tttt) cc_final: 0.7680 (ttmm)
REVERT: A  391 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7487 (mm-30)
REVERT: A  430 THR cc_start: 0.8060 (m) cc_final: 0.7461 (p)
REVERT: A  455 GLU cc_start: 0.7188 (tt0) cc_final: 0.6985 (tt0)
REVERT: A  479 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7610 (pttt)
REVERT: A  487 LYS cc_start: 0.7102 (mtmm) cc_final: 0.6756 (mtmm)
REVERT: A  584 HIS cc_start: 0.5981 (m90) cc_final: 0.5693 (m170)
REVERT: A  593 LYS cc_start: 0.6656 (tptp) cc_final: 0.6173 (tptp)
  outliers start: 32
  outliers final: 21
  residues processed: 262
  average time/residue: 0.2619
  time to fit residues: 92.1800
Evaluate side-chains
  260 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 237
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  538 GLN
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  479 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 100 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 112 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  48 HIS
B  81 GLN
A 444 ASN
** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.5283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.082   9420  Z= 0.430
  Angle     :  0.740   9.345  12769  Z= 0.378
  Chirality :  0.054   0.431   1425
  Planarity :  0.005   0.047   1679
  Dihedral  :  7.134  56.910   1414
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 13.56 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.67 (0.22), residues: 1170
  helix: -2.57 (0.61), residues: 53
  sheet: -2.34 (0.50), residues: 82
  loop : -1.87 (0.18), residues: 1035

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP C  49 
 HIS   0.008   0.002   HIS A 507 
 PHE   0.024   0.002   PHE A 481 
 TYR   0.017   0.002   TYR B  50 
 ARG   0.008   0.001   ARG B  47 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 271
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 GLN cc_start: 0.6609 (pp30) cc_final: 0.6348 (pp30)
REVERT: B   30 ASP cc_start: 0.7699 (t70) cc_final: 0.7095 (t70)
REVERT: B  112 TYR cc_start: 0.7515 (m-80) cc_final: 0.7239 (m-80)
REVERT: B  138 ARG cc_start: 0.6702 (mmm160) cc_final: 0.5583 (mmm160)
REVERT: B  139 GLU cc_start: 0.6666 (mp0) cc_final: 0.6290 (mp0)
REVERT: B  147 GLU cc_start: 0.6713 (tp30) cc_final: 0.6254 (tp30)
REVERT: B  164 GLN cc_start: 0.7681 (pm20) cc_final: 0.7150 (pm20)
REVERT: B  190 ARG cc_start: 0.6886 (ttt-90) cc_final: 0.6369 (ttt-90)
REVERT: B  274 TYR cc_start: 0.7864 (t80) cc_final: 0.7630 (t80)
REVERT: B  284 ASN cc_start: 0.7967 (t0) cc_final: 0.7647 (t0)
REVERT: B  405 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6311 (tm-30)
REVERT: B  421 ASP cc_start: 0.6713 (p0) cc_final: 0.6359 (p0)
REVERT: B  441 TYR cc_start: 0.8387 (m-80) cc_final: 0.8060 (m-80)
REVERT: B  450 ILE cc_start: 0.8134 (tt) cc_final: 0.7922 (pt)
REVERT: B  538 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.6333 (pm20)
REVERT: A   45 GLU cc_start: 0.7291 (mp0) cc_final: 0.7054 (mp0)
REVERT: A   46 ASP cc_start: 0.7658 (t70) cc_final: 0.7167 (t0)
REVERT: A  142 GLU cc_start: 0.6978 (tt0) cc_final: 0.6582 (tt0)
REVERT: A  148 VAL cc_start: 0.8397 (t) cc_final: 0.8053 (m)
REVERT: A  160 GLU cc_start: 0.7827 (pm20) cc_final: 0.7515 (pm20)
REVERT: A  198 SER cc_start: 0.8327 (m) cc_final: 0.7596 (p)
REVERT: A  250 VAL cc_start: 0.8040 (t) cc_final: 0.7719 (m)
REVERT: A  261 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7401 (ptpp)
REVERT: A  263 THR cc_start: 0.7879 (m) cc_final: 0.7628 (p)
REVERT: A  292 VAL cc_start: 0.8122 (m) cc_final: 0.7834 (p)
REVERT: A  325 LYS cc_start: 0.7116 (mttt) cc_final: 0.6709 (mtmt)
REVERT: A  358 HIS cc_start: 0.7722 (m90) cc_final: 0.7283 (m90)
REVERT: A  360 LYS cc_start: 0.8024 (tttt) cc_final: 0.7602 (ttmm)
REVERT: A  391 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7687 (mm-30)
REVERT: A  430 THR cc_start: 0.8039 (m) cc_final: 0.7426 (p)
REVERT: A  479 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7883 (pttt)
REVERT: A  489 LYS cc_start: 0.8065 (tttt) cc_final: 0.7752 (tttm)
REVERT: A  524 VAL cc_start: 0.8339 (t) cc_final: 0.8084 (p)
REVERT: A  593 LYS cc_start: 0.6740 (tptp) cc_final: 0.6509 (tptp)
  outliers start: 34
  outliers final: 24
  residues processed: 284
  average time/residue: 0.2489
  time to fit residues: 93.4874
Evaluate side-chains
  276 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 249
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 CYS
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  538 GLN
Chi-restraints excluded: chain B residue  553 GLU
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  261 LYS
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  515 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 63 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 94 optimal weight:    0.4980
   chunk 62 optimal weight:    0.6980
   chunk 111 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0370
   chunk 44 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 422 ASN
A 444 ASN
A 559 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.5522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9420  Z= 0.301
  Angle     :  0.681   9.384  12769  Z= 0.346
  Chirality :  0.051   0.428   1425
  Planarity :  0.004   0.040   1679
  Dihedral  :  6.965  56.380   1414
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 15.80 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.23), residues: 1170
  helix: -2.52 (0.58), residues: 60
  sheet: -2.53 (0.48), residues: 90
  loop : -1.82 (0.18), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP C  49 
 HIS   0.006   0.001   HIS A 507 
 PHE   0.014   0.002   PHE A 481 
 TYR   0.017   0.002   TYR A 316 
 ARG   0.008   0.001   ARG B  47 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 246
  time to evaluate  : 1.187 
Fit side-chains
REVERT: B   24 GLN cc_start: 0.6582 (pp30) cc_final: 0.6334 (pp30)
REVERT: B   30 ASP cc_start: 0.7700 (t70) cc_final: 0.7085 (t70)
REVERT: B  138 ARG cc_start: 0.6723 (mmm160) cc_final: 0.5643 (mmm160)
REVERT: B  139 GLU cc_start: 0.6644 (mp0) cc_final: 0.6241 (mp0)
REVERT: B  147 GLU cc_start: 0.6749 (tp30) cc_final: 0.6270 (tp30)
REVERT: B  190 ARG cc_start: 0.6963 (ttt-90) cc_final: 0.6438 (ttt-90)
REVERT: B  274 TYR cc_start: 0.7941 (t80) cc_final: 0.7721 (t80)
REVERT: B  282 MET cc_start: 0.6792 (mtm) cc_final: 0.6546 (mtm)
REVERT: B  284 ASN cc_start: 0.7953 (t0) cc_final: 0.7648 (t0)
REVERT: B  405 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6365 (tm-30)
REVERT: B  421 ASP cc_start: 0.6734 (p0) cc_final: 0.6370 (p0)
REVERT: B  441 TYR cc_start: 0.8340 (m-80) cc_final: 0.7997 (m-80)
REVERT: B  460 GLU cc_start: 0.7116 (tt0) cc_final: 0.6539 (tt0)
REVERT: B  538 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.6297 (pm20)
REVERT: B  568 GLN cc_start: 0.7041 (tm-30) cc_final: 0.6637 (tm-30)
REVERT: A   46 ASP cc_start: 0.7604 (t70) cc_final: 0.7158 (t0)
REVERT: A   97 GLU cc_start: 0.6623 (mp0) cc_final: 0.6391 (mp0)
REVERT: A  142 GLU cc_start: 0.6891 (tt0) cc_final: 0.6562 (tt0)
REVERT: A  148 VAL cc_start: 0.8330 (t) cc_final: 0.8024 (m)
REVERT: A  198 SER cc_start: 0.8361 (m) cc_final: 0.7614 (p)
REVERT: A  250 VAL cc_start: 0.8033 (t) cc_final: 0.7761 (m)
REVERT: A  263 THR cc_start: 0.7929 (m) cc_final: 0.7671 (p)
REVERT: A  292 VAL cc_start: 0.8080 (m) cc_final: 0.7783 (p)
REVERT: A  318 MET cc_start: 0.6382 (tpp) cc_final: 0.6173 (tpp)
REVERT: A  325 LYS cc_start: 0.7037 (mttt) cc_final: 0.6658 (mtmt)
REVERT: A  399 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7555 (mtpp)
REVERT: A  430 THR cc_start: 0.8011 (m) cc_final: 0.7399 (p)
REVERT: A  442 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7928 (t)
REVERT: A  479 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7947 (pttt)
REVERT: A  489 LYS cc_start: 0.8009 (tttt) cc_final: 0.7592 (tttp)
REVERT: A  593 LYS cc_start: 0.6718 (tptp) cc_final: 0.6473 (tptp)
  outliers start: 38
  outliers final: 25
  residues processed: 263
  average time/residue: 0.2565
  time to fit residues: 90.7225
Evaluate side-chains
  271 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 243
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 CYS
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  538 GLN
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  480 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0980
   chunk 55 optimal weight:    0.0770
   chunk 10 optimal weight:    0.4980
   chunk 87 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 97 optimal weight:    0.4980
   chunk 104 optimal weight:    0.0470
   overall best weight:    0.2436

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

Flipped N/Q/H residues before XYZ refinement:
B 530 ASN
A 271 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.5581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9420  Z= 0.207
  Angle     :  0.637   9.376  12769  Z= 0.323
  Chirality :  0.048   0.421   1425
  Planarity :  0.004   0.038   1679
  Dihedral  :  6.650  56.817   1414
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.68 %
    Favored  : 80.20 %
  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: -2.55 (0.23), residues: 1170
  helix: -2.35 (0.61), residues: 60
  sheet: -2.70 (0.45), residues: 102
  loop : -1.70 (0.19), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP C  49 
 HIS   0.006   0.001   HIS A 507 
 PHE   0.011   0.001   PHE A 481 
 TYR   0.022   0.002   TYR B 112 
 ARG   0.008   0.001   ARG B 188 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 243
  time to evaluate  : 0.844 
Fit side-chains
REVERT: B   30 ASP cc_start: 0.7655 (t70) cc_final: 0.7069 (t70)
REVERT: B  138 ARG cc_start: 0.6755 (mmm160) cc_final: 0.5817 (mmm160)
REVERT: B  139 GLU cc_start: 0.6655 (mp0) cc_final: 0.6253 (mp0)
REVERT: B  147 GLU cc_start: 0.6721 (tp30) cc_final: 0.6293 (tp30)
REVERT: B  190 ARG cc_start: 0.6945 (ttt-90) cc_final: 0.6485 (ttt-90)
REVERT: B  274 TYR cc_start: 0.7948 (t80) cc_final: 0.7597 (t80)
REVERT: B  282 MET cc_start: 0.6808 (mtm) cc_final: 0.6575 (mtm)
REVERT: B  284 ASN cc_start: 0.7909 (t0) cc_final: 0.7597 (t0)
REVERT: B  297 THR cc_start: 0.8430 (m) cc_final: 0.8184 (p)
REVERT: B  321 GLU cc_start: 0.6079 (tt0) cc_final: 0.5817 (tt0)
REVERT: B  405 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6362 (tm-30)
REVERT: B  421 ASP cc_start: 0.6770 (p0) cc_final: 0.6398 (p0)
REVERT: B  441 TYR cc_start: 0.8290 (m-80) cc_final: 0.7934 (m-80)
REVERT: B  460 GLU cc_start: 0.7157 (tt0) cc_final: 0.6549 (tt0)
REVERT: B  514 LEU cc_start: 0.7191 (mp) cc_final: 0.6859 (mt)
REVERT: B  538 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.6182 (pm20)
REVERT: A   28 LYS cc_start: 0.8014 (mmtp) cc_final: 0.7703 (mmtt)
REVERT: A   46 ASP cc_start: 0.7582 (t70) cc_final: 0.7152 (t0)
REVERT: A   98 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7783 (mtp180)
REVERT: A  142 GLU cc_start: 0.6903 (tt0) cc_final: 0.6597 (tt0)
REVERT: A  148 VAL cc_start: 0.8374 (t) cc_final: 0.8042 (m)
REVERT: A  158 ASN cc_start: 0.6963 (m110) cc_final: 0.6667 (m110)
REVERT: A  166 ASP cc_start: 0.7369 (t70) cc_final: 0.7043 (t70)
REVERT: A  198 SER cc_start: 0.8355 (m) cc_final: 0.7685 (p)
REVERT: A  261 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7186 (ptpp)
REVERT: A  263 THR cc_start: 0.7916 (m) cc_final: 0.7665 (p)
REVERT: A  292 VAL cc_start: 0.8028 (m) cc_final: 0.7681 (p)
REVERT: A  318 MET cc_start: 0.6396 (tpp) cc_final: 0.6177 (tpp)
REVERT: A  325 LYS cc_start: 0.6987 (mttt) cc_final: 0.6723 (mtmt)
REVERT: A  360 LYS cc_start: 0.7990 (tttt) cc_final: 0.7637 (ttmm)
REVERT: A  399 LYS cc_start: 0.7787 (ttmm) cc_final: 0.7479 (mtpp)
REVERT: A  430 THR cc_start: 0.7989 (m) cc_final: 0.7380 (p)
REVERT: A  442 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7844 (t)
REVERT: A  479 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7840 (pttt)
REVERT: A  489 LYS cc_start: 0.8000 (tttt) cc_final: 0.7762 (tttm)
REVERT: A  551 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6626 (tm-30)
REVERT: A  593 LYS cc_start: 0.6707 (tptp) cc_final: 0.6430 (tptp)
  outliers start: 32
  outliers final: 22
  residues processed: 258
  average time/residue: 0.2415
  time to fit residues: 82.4233
Evaluate side-chains
  264 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 238
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  538 GLN
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  261 LYS
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  468 ASN
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  515 CYS
Chi-restraints excluded: chain A residue  524 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0970
   chunk 31 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 98 optimal weight:    0.7980
   chunk 103 optimal weight:    0.0270
   chunk 68 optimal weight:    0.3980
   chunk 110 optimal weight:    0.9990
   chunk 67 optimal weight:    0.4980
   overall best weight:    0.3236

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

Flipped N/Q/H residues before XYZ refinement:
B  54 GLN
B 530 ASN
A 304 HIS
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.5736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9420  Z= 0.237
  Angle     :  0.650   9.366  12769  Z= 0.330
  Chirality :  0.049   0.417   1425
  Planarity :  0.004   0.037   1679
  Dihedral  :  6.609  56.300   1414
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.98 %
    Favored  : 80.00 %
  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: -2.43 (0.23), residues: 1170
  helix: -2.31 (0.63), residues: 54
  sheet: -2.58 (0.43), residues: 112
  loop : -1.60 (0.19), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP C  49 
 HIS   0.006   0.001   HIS A 507 
 PHE   0.013   0.001   PHE A 481 
 TYR   0.016   0.002   TYR B 112 
 ARG   0.005   0.001   ARG A 138 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 241
  time to evaluate  : 1.172 
Fit side-chains
REVERT: B   30 ASP cc_start: 0.7695 (t70) cc_final: 0.7123 (t70)
REVERT: B  138 ARG cc_start: 0.6764 (mmm160) cc_final: 0.5829 (mmm160)
REVERT: B  139 GLU cc_start: 0.6739 (mp0) cc_final: 0.6334 (mp0)
REVERT: B  190 ARG cc_start: 0.7142 (ttt-90) cc_final: 0.6586 (ttt-90)
REVERT: B  274 TYR cc_start: 0.7915 (t80) cc_final: 0.7596 (t80)
REVERT: B  282 MET cc_start: 0.6798 (mtm) cc_final: 0.6573 (mtm)
REVERT: B  284 ASN cc_start: 0.8018 (t0) cc_final: 0.7489 (t0)
REVERT: B  297 THR cc_start: 0.8491 (m) cc_final: 0.8273 (p)
REVERT: B  321 GLU cc_start: 0.6108 (tt0) cc_final: 0.5881 (tt0)
REVERT: B  404 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6610 (mt-10)
REVERT: B  405 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6386 (tm-30)
REVERT: B  421 ASP cc_start: 0.6767 (p0) cc_final: 0.6392 (p0)
REVERT: B  441 TYR cc_start: 0.8286 (m-80) cc_final: 0.7954 (m-80)
REVERT: B  460 GLU cc_start: 0.7159 (tt0) cc_final: 0.6536 (tt0)
REVERT: B  514 LEU cc_start: 0.7207 (mp) cc_final: 0.6885 (mt)
REVERT: B  538 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.6248 (pm20)
REVERT: B  568 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6736 (tm-30)
REVERT: A   28 LYS cc_start: 0.8013 (mmtp) cc_final: 0.7693 (mmtt)
REVERT: A   46 ASP cc_start: 0.7585 (t70) cc_final: 0.7143 (t0)
REVERT: A   98 ARG cc_start: 0.8002 (mtp-110) cc_final: 0.7743 (mtp180)
REVERT: A  142 GLU cc_start: 0.6896 (tt0) cc_final: 0.6600 (tt0)
REVERT: A  148 VAL cc_start: 0.8328 (t) cc_final: 0.7996 (m)
REVERT: A  158 ASN cc_start: 0.6921 (m110) cc_final: 0.6665 (m110)
REVERT: A  198 SER cc_start: 0.8279 (m) cc_final: 0.7558 (p)
REVERT: A  261 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7119 (ptpp)
REVERT: A  263 THR cc_start: 0.7929 (m) cc_final: 0.7671 (p)
REVERT: A  292 VAL cc_start: 0.8003 (m) cc_final: 0.7714 (p)
REVERT: A  325 LYS cc_start: 0.7009 (mttt) cc_final: 0.6706 (mtmt)
REVERT: A  399 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7490 (mtpp)
REVERT: A  430 THR cc_start: 0.8014 (m) cc_final: 0.7402 (p)
REVERT: A  593 LYS cc_start: 0.6735 (tptp) cc_final: 0.6434 (tptp)
  outliers start: 31
  outliers final: 26
  residues processed: 252
  average time/residue: 0.2438
  time to fit residues: 81.5618
Evaluate side-chains
  268 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 240
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   54 GLN
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  538 GLN
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  261 LYS
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  277 MET
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  473 ASN
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  540 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 76 optimal weight:    0.0370
   chunk 115 optimal weight:    0.9990
   chunk 106 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
B 478 HIS
B 530 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.5955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   9420  Z= 0.338
  Angle     :  0.700   9.354  12769  Z= 0.356
  Chirality :  0.052   0.422   1425
  Planarity :  0.004   0.039   1679
  Dihedral  :  6.848  56.092   1414
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.85 %
    Favored  : 79.61 %
  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: -2.50 (0.23), residues: 1170
  helix: -2.42 (0.62), residues: 54
  sheet: -2.61 (0.48), residues: 92
  loop : -1.68 (0.19), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP C  49 
 HIS   0.008   0.001   HIS A 507 
 PHE   0.017   0.002   PHE A 481 
 TYR   0.028   0.002   TYR A 125 
 ARG   0.007   0.001   ARG A 138 

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 249
  time to evaluate  : 1.097 
Fit side-chains
REVERT: B   30 ASP cc_start: 0.7726 (t70) cc_final: 0.7149 (t70)
REVERT: B  138 ARG cc_start: 0.6763 (mmm160) cc_final: 0.5830 (mmm160)
REVERT: B  139 GLU cc_start: 0.6811 (mp0) cc_final: 0.6399 (mp0)
REVERT: B  147 GLU cc_start: 0.7139 (tp30) cc_final: 0.6415 (tp30)
REVERT: B  190 ARG cc_start: 0.7411 (ttt-90) cc_final: 0.6756 (ttt-90)
REVERT: B  274 TYR cc_start: 0.7917 (t80) cc_final: 0.7614 (t80)
REVERT: B  282 MET cc_start: 0.6790 (mtm) cc_final: 0.6560 (mtm)
REVERT: B  284 ASN cc_start: 0.8083 (t0) cc_final: 0.7784 (t0)
REVERT: B  289 TYR cc_start: 0.8416 (m-80) cc_final: 0.7878 (m-80)
REVERT: B  297 THR cc_start: 0.8557 (m) cc_final: 0.8331 (p)
REVERT: B  321 GLU cc_start: 0.6126 (tt0) cc_final: 0.5909 (tt0)
REVERT: B  405 GLU cc_start: 0.6762 (tm-30) cc_final: 0.6402 (tm-30)
REVERT: B  421 ASP cc_start: 0.6766 (p0) cc_final: 0.6348 (p0)
REVERT: B  441 TYR cc_start: 0.8329 (m-80) cc_final: 0.8001 (m-80)
REVERT: B  460 GLU cc_start: 0.7133 (tt0) cc_final: 0.6554 (tt0)
REVERT: B  514 LEU cc_start: 0.7248 (mp) cc_final: 0.6925 (mt)
REVERT: B  538 GLN cc_start: 0.6487 (OUTLIER) cc_final: 0.6262 (pm20)
REVERT: B  568 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6666 (tm-30)
REVERT: A   28 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7722 (mmtt)
REVERT: A   46 ASP cc_start: 0.7591 (t70) cc_final: 0.7149 (t0)
REVERT: A   98 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7665 (mtp180)
REVERT: A  142 GLU cc_start: 0.6906 (tt0) cc_final: 0.6566 (tt0)
REVERT: A  148 VAL cc_start: 0.8336 (t) cc_final: 0.8010 (m)
REVERT: A  158 ASN cc_start: 0.6958 (m110) cc_final: 0.6694 (m110)
REVERT: A  198 SER cc_start: 0.8364 (m) cc_final: 0.7645 (p)
REVERT: A  261 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7220 (ptpt)
REVERT: A  263 THR cc_start: 0.7937 (m) cc_final: 0.7693 (p)
REVERT: A  292 VAL cc_start: 0.8009 (m) cc_final: 0.7728 (p)
REVERT: A  325 LYS cc_start: 0.7110 (mttt) cc_final: 0.6799 (mtmt)
REVERT: A  360 LYS cc_start: 0.7995 (tttt) cc_final: 0.7631 (ttmm)
REVERT: A  377 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6943 (ttp-170)
REVERT: A  399 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7546 (mtpp)
REVERT: A  430 THR cc_start: 0.8048 (m) cc_final: 0.7442 (p)
REVERT: A  584 HIS cc_start: 0.5952 (m90) cc_final: 0.5605 (m170)
REVERT: A  593 LYS cc_start: 0.6751 (tptp) cc_final: 0.6218 (tptp)
  outliers start: 26
  outliers final: 23
  residues processed: 260
  average time/residue: 0.2334
  time to fit residues: 80.9014
Evaluate side-chains
  274 residues out of total 1025 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 249
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  538 GLN
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  261 LYS
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  487 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0010
   chunk 11 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 80 optimal weight:    0.1980
   chunk 5 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 498 ASN
B 530 ASN
A 152 ASN
A 163 GLN
A 196 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.144199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.122010 restraints weight = 13324.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.69
r_work: 0.3448 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.6035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9420  Z= 0.253
  Angle     :  0.675   9.425  12769  Z= 0.343
  Chirality :  0.049   0.417   1425
  Planarity :  0.004   0.037   1679
  Dihedral  :  6.727  55.736   1414
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.02 %
    Favored  : 78.54 %
  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: -2.52 (0.23), residues: 1170
  helix: -2.60 (0.55), residues: 64
  sheet: -2.73 (0.46), residues: 102
  loop : -1.64 (0.19), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP C  49 
 HIS   0.006   0.001   HIS A 507 
 PHE   0.011   0.001   PHE A 481 
 TYR   0.025   0.002   TYR A 125 
 ARG   0.006   0.001   ARG B 100 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2853.75 seconds
wall clock time: 51 minutes 54.50 seconds (3114.50 seconds total)