Starting phenix.real_space_refine
on Thu Mar 13 22:14:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avw_15685/03_2025/8avw_15685.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avw_15685/03_2025/8avw_15685.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8avw_15685/03_2025/8avw_15685.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avw_15685/03_2025/8avw_15685.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avw_15685/03_2025/8avw_15685.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avw_15685/03_2025/8avw_15685.cif"
  }
  resolution = 3.62
  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=   0.012
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      24      5.16       5
     C    5706      2.51       5
     N    1602      2.21       5
     O    1660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8992
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 577, 4448
          Classifications: {'peptide': 577}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 531}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4458
          Classifications: {'peptide': 579}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 533}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.13, per 1000 atoms: 0.79
  Number of scatterers: 8992
  At special positions: 0
  Unit cell: (93.9253, 98.2338, 174.925, 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      24     16.00
     O    1660      8.00
     N    1602      7.00
     C    5706      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.07
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 8 sheets defined
      43.1% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 63
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 3.654A  pdb=" N   ARG A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 78
      removed outlier: 3.824A  pdb=" N   LEU A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 89
      removed outlier: 3.764A  pdb=" N   ALA A  87 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 148
      removed outlier: 3.535A  pdb=" N   PHE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 209 through 216
    Processing helix  chain 'A' and resid 257 through 268
      removed outlier: 3.713A  pdb=" N   GLN A 262 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TYR A 263 " --> pdb=" O   MET A 259 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 264 " --> pdb=" O   HIS A 260 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ARG A 265 " --> pdb=" O   MET A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 331
      removed outlier: 4.220A  pdb=" N   THR A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 308 " --> pdb=" O   THR A 304 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   GLN A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL A 318 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA A 321 " --> pdb=" O   GLN A 317 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL A 324 " --> pdb=" O   GLU A 320 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN A 329 " --> pdb=" O   ALA A 325 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   SER A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LEU A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 342
      removed outlier: 3.673A  pdb=" N   ARG A 337 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL A 338 " --> pdb=" O   HIS A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 353
      removed outlier: 3.837A  pdb=" N   SER A 353 " --> pdb=" O   HIS A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 396
      removed outlier: 3.521A  pdb=" N   VAL A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP A 389 " --> pdb=" O   ALA A 385 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA A 393 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   TRP A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 412
      removed outlier: 4.361A  pdb=" N   LEU A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 416
      removed outlier: 3.661A  pdb=" N   ALA A 416 " --> pdb=" O   PRO A 413 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 413 through 416'
    Processing helix  chain 'A' and resid 455 through 459
      removed outlier: 3.605A  pdb=" N   ALA A 459 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 499
      removed outlier: 3.679A  pdb=" N   ILE A 488 " --> pdb=" O   HIS A 484 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ASP A 493 " --> pdb=" O   GLU A 489 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP A 496 " --> pdb=" O   GLN A 492 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   THR A 497 " --> pdb=" O   ASP A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 543
      removed outlier: 3.638A  pdb=" N   SER A 507 " --> pdb=" O   GLY A 503 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL A 508 " --> pdb=" O   GLU A 504 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE A 509 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ASP A 511 " --> pdb=" O   SER A 507 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 516 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR A 517 " --> pdb=" O   ASN A 513 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN A 518 " --> pdb=" O   ARG A 514 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 528 " --> pdb=" O   ARG A 524 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   SER A 531 " --> pdb=" O   GLY A 527 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN A 535 " --> pdb=" O   SER A 531 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLU A 536 " --> pdb=" O   HIS A 532 " (cutoff:3.500A)
      Proline residue:  A 537  - end of helix
    Processing helix  chain 'A' and resid 546 through 551
    Processing helix  chain 'A' and resid 563 through 591
      removed outlier: 3.827A  pdb=" N   ARG A 573 " --> pdb=" O   GLY A 569 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLU A 574 " --> pdb=" O   PHE A 570 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN A 583 " --> pdb=" O   ARG A 579 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   HIS A 586 " --> pdb=" O   THR A 582 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR A 587 " --> pdb=" O   GLN A 583 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   THR A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 3.654A  pdb=" N   ARG B  70 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 78
      removed outlier: 3.827A  pdb=" N   LEU B  77 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 89
      removed outlier: 3.766A  pdb=" N   ALA B  87 " --> pdb=" O   PRO B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 148
      removed outlier: 3.544A  pdb=" N   PHE B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 169
    Processing helix  chain 'B' and resid 209 through 216
    Processing helix  chain 'B' and resid 257 through 268
      removed outlier: 3.713A  pdb=" N   GLN B 262 " --> pdb=" O   PRO B 258 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   TYR B 263 " --> pdb=" O   MET B 259 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU B 264 " --> pdb=" O   HIS B 260 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG B 265 " --> pdb=" O   MET B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 331
      removed outlier: 4.199A  pdb=" N   THR B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU B 308 " --> pdb=" O   THR B 304 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   GLN B 317 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL B 318 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA B 321 " --> pdb=" O   GLN B 317 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLN B 329 " --> pdb=" O   ALA B 325 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LEU B 331 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 342
      removed outlier: 3.687A  pdb=" N   ARG B 337 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL B 338 " --> pdb=" O   HIS B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 353
      removed outlier: 3.837A  pdb=" N   SER B 353 " --> pdb=" O   HIS B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 396
      removed outlier: 3.524A  pdb=" N   VAL B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ASP B 389 " --> pdb=" O   ALA B 385 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA B 393 " --> pdb=" O   ASP B 389 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   TRP B 394 " --> pdb=" O   ALA B 390 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 412
      removed outlier: 4.371A  pdb=" N   LEU B 411 " --> pdb=" O   ALA B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 416
      removed outlier: 3.659A  pdb=" N   ALA B 416 " --> pdb=" O   PRO B 413 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 413 through 416'
    Processing helix  chain 'B' and resid 455 through 459
      removed outlier: 3.605A  pdb=" N   ALA B 459 " --> pdb=" O   PRO B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 499
      removed outlier: 3.678A  pdb=" N   ILE B 488 " --> pdb=" O   HIS B 484 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASP B 493 " --> pdb=" O   GLU B 489 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP B 496 " --> pdb=" O   GLN B 492 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   THR B 497 " --> pdb=" O   ASP B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 543
      removed outlier: 3.507A  pdb=" N   ARG B 505 " --> pdb=" O   ALA B 501 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   SER B 507 " --> pdb=" O   GLY B 503 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL B 508 " --> pdb=" O   GLU B 504 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ILE B 509 " --> pdb=" O   ARG B 505 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ASP B 511 " --> pdb=" O   SER B 507 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 516 " --> pdb=" O   LEU B 512 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR B 517 " --> pdb=" O   ASN B 513 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN B 518 " --> pdb=" O   ARG B 514 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   SER B 519 " --> pdb=" O   ALA B 515 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE B 528 " --> pdb=" O   ARG B 524 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   SER B 531 " --> pdb=" O   GLY B 527 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLN B 535 " --> pdb=" O   SER B 531 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLU B 536 " --> pdb=" O   HIS B 532 " (cutoff:3.500A)
      Proline residue:  B 537  - end of helix
    Processing helix  chain 'B' and resid 546 through 551
    Processing helix  chain 'B' and resid 563 through 591
      removed outlier: 3.833A  pdb=" N   ARG B 573 " --> pdb=" O   GLY B 569 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU B 574 " --> pdb=" O   PHE B 570 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN B 583 " --> pdb=" O   ARG B 579 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   HIS B 586 " --> pdb=" O   THR B 582 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR B 587 " --> pdb=" O   GLN B 583 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR B 589 " --> pdb=" O   LEU B 585 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.676A  pdb=" N   THR A  43 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   MET A  54 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU A  41 " --> pdb=" O   MET A  54 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A 111 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203
      removed outlier: 6.881A  pdb=" N   LEU A 175 " --> pdb=" O   ILE A 187 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   VAL A 173 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   TRP A 284 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   VAL A 277 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   LEU A 286 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   VAL A 275 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ALA A 288 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LEU A 273 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   HIS A 290 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   SER A 271 " --> pdb=" O   HIS A 290 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ARG A 222 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 380
      removed outlier: 4.101A  pdb=" N   PHE A 372 " --> pdb=" O   ARG A 375 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   GLU A 436 " --> pdb=" O   VAL A 430 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 447 through 452
      removed outlier: 4.010A  pdb=" N   LEU A 447 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35
      removed outlier: 6.668A  pdb=" N   THR B  43 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   MET B  54 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LEU B  41 " --> pdb=" O   MET B  54 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU B 111 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203
      removed outlier: 6.881A  pdb=" N   LEU B 175 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   GLU B 189 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   VAL B 173 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   TRP B 284 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   VAL B 277 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   VAL B 275 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ALA B 288 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LEU B 273 " --> pdb=" O   ALA B 288 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   HIS B 290 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   SER B 271 " --> pdb=" O   HIS B 290 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG B 222 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 375 through 380
      removed outlier: 4.102A  pdb=" N   PHE B 372 " --> pdb=" O   ARG B 375 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   GLU B 436 " --> pdb=" O   VAL B 430 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 445 through 452
      removed outlier: 7.252A  pdb=" N   LEU B 445 " --> pdb=" O   GLY B 478 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   GLY B 478 " --> pdb=" O   LEU B 445 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU B 447 " --> pdb=" O   LYS B 476 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1068 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: 2.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1910
        1.34 -     1.46: 3087
        1.46 -     1.58: 4186
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 9223
  Sorted by residual:
  bond pdb=" C2D LBV A1000 "
       pdb=" C3D LBV A1000 "
    ideal  model  delta    sigma   weight residual
    1.358  1.432 -0.074 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C2D LBV B1000 "
       pdb=" C3D LBV B1000 "
    ideal  model  delta    sigma   weight residual
    1.358  1.430 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C4C LBV A1000 "
       pdb=" CHD LBV A1000 "
    ideal  model  delta    sigma   weight residual
    1.428  1.357  0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" C4C LBV B1000 "
       pdb=" CHD LBV B1000 "
    ideal  model  delta    sigma   weight residual
    1.428  1.359  0.069 2.00e-02 2.50e+03 1.18e+01
  bond pdb=" C   SER B 558 "
       pdb=" N   PRO B 559 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 8.40e-03 1.42e+04 1.12e+01
  ... (remaining 9218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 8965
        1.36 -     2.72: 2797
        2.72 -     4.07: 757
        4.07 -     5.43: 83
        5.43 -     6.79: 9
  Bond angle restraints: 12611
  Sorted by residual:
  angle pdb=" N   GLN A 329 "
        pdb=" CA  GLN A 329 "
        pdb=" C   GLN A 329 "
      ideal   model   delta    sigma   weight residual
     114.04  108.55    5.49 1.24e+00 6.50e-01 1.96e+01
  angle pdb=" N   GLN B 329 "
        pdb=" CA  GLN B 329 "
        pdb=" C   GLN B 329 "
      ideal   model   delta    sigma   weight residual
     114.04  108.56    5.48 1.24e+00 6.50e-01 1.95e+01
  angle pdb=" N   LEU B 360 "
        pdb=" CA  LEU B 360 "
        pdb=" C   LEU B 360 "
      ideal   model   delta    sigma   weight residual
     114.56  109.47    5.09 1.27e+00 6.20e-01 1.61e+01
  angle pdb=" N   LEU A 360 "
        pdb=" CA  LEU A 360 "
        pdb=" C   LEU A 360 "
      ideal   model   delta    sigma   weight residual
     114.56  109.55    5.01 1.27e+00 6.20e-01 1.55e+01
  angle pdb=" C   LEU B 297 "
        pdb=" N   PRO B 298 "
        pdb=" CA  PRO B 298 "
      ideal   model   delta    sigma   weight residual
     119.66  122.52   -2.86 7.30e-01 1.88e+00 1.54e+01
  ... (remaining 12606 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.85: 4637
       15.85 -    31.71: 575
       31.71 -    47.56: 176
       47.56 -    63.41: 99
       63.41 -    79.27: 32
  Dihedral angle restraints: 5519
    sinusoidal: 2210
      harmonic: 3309
  Sorted by residual:
  dihedral pdb=" CA  HIS B 219 "
           pdb=" C   HIS B 219 "
           pdb=" N   LEU B 220 "
           pdb=" CA  LEU B 220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.34  -22.66     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  HIS A 219 "
           pdb=" C   HIS A 219 "
           pdb=" N   LEU A 220 "
           pdb=" CA  LEU A 220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.70  -22.30     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" C   ASN A 243 "
           pdb=" N   ASN A 243 "
           pdb=" CA  ASN A 243 "
           pdb=" CB  ASN A 243 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.77    9.17     0      2.50e+00 1.60e-01 1.35e+01
  ... (remaining 5516 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 771
       0.058 -    0.116: 394
       0.116 -    0.175: 186
       0.175 -    0.233: 48
       0.233 -    0.291: 13
  Chirality restraints: 1412
  Sorted by residual:
  chirality pdb=" CA  ASN A 243 "
            pdb=" N   ASN A 243 "
            pdb=" C   ASN A 243 "
            pdb=" CB  ASN A 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  GLN B 551 "
            pdb=" N   GLN B 551 "
            pdb=" C   GLN B 551 "
            pdb=" CB  GLN B 551 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CA  ASN B 243 "
            pdb=" N   ASN B 243 "
            pdb=" C   ASN B 243 "
            pdb=" CB  ASN B 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 1409 not shown)

  Planarity restraints: 1657
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C LBV A1000 "    0.063 2.00e-02 2.50e+03   2.16e-01 1.05e+03
        pdb=" C2C LBV A1000 "   -0.100 2.00e-02 2.50e+03
        pdb=" C3C LBV A1000 "    0.083 2.00e-02 2.50e+03
        pdb=" C4C LBV A1000 "   -0.068 2.00e-02 2.50e+03
        pdb=" CAC LBV A1000 "   -0.376 2.00e-02 2.50e+03
        pdb=" CHC LBV A1000 "    0.254 2.00e-02 2.50e+03
        pdb=" CHD LBV A1000 "   -0.218 2.00e-02 2.50e+03
        pdb=" CMC LBV A1000 "    0.377 2.00e-02 2.50e+03
        pdb=" N_C LBV A1000 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C LBV B1000 "    0.052 2.00e-02 2.50e+03   1.63e-01 5.97e+02
        pdb=" C2C LBV B1000 "   -0.073 2.00e-02 2.50e+03
        pdb=" C3C LBV B1000 "    0.063 2.00e-02 2.50e+03
        pdb=" C4C LBV B1000 "   -0.054 2.00e-02 2.50e+03
        pdb=" CAC LBV B1000 "   -0.282 2.00e-02 2.50e+03
        pdb=" CHC LBV B1000 "    0.173 2.00e-02 2.50e+03
        pdb=" CHD LBV B1000 "   -0.181 2.00e-02 2.50e+03
        pdb=" CMC LBV B1000 "    0.286 2.00e-02 2.50e+03
        pdb=" N_C LBV B1000 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1D LBV B1000 "   -0.010 2.00e-02 2.50e+03   1.47e-01 4.89e+02
        pdb=" C2D LBV B1000 "   -0.044 2.00e-02 2.50e+03
        pdb=" C3D LBV B1000 "    0.014 2.00e-02 2.50e+03
        pdb=" C4D LBV B1000 "   -0.035 2.00e-02 2.50e+03
        pdb=" CAD LBV B1000 "    0.102 2.00e-02 2.50e+03
        pdb=" CHD LBV B1000 "    0.257 2.00e-02 2.50e+03
        pdb=" CMD LBV B1000 "   -0.102 2.00e-02 2.50e+03
        pdb=" N_D LBV B1000 "   -0.301 2.00e-02 2.50e+03
        pdb=" O_D LBV B1000 "    0.121 2.00e-02 2.50e+03
  ... (remaining 1654 not shown)

  Histogram of nonbonded interaction distances:
        2.60 -     3.06: 4021
        3.06 -     3.52: 9099
        3.52 -     3.98: 13399
        3.98 -     4.44: 15372
        4.44 -     4.90: 25170
  Nonbonded interactions: 67061
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 527 "
            pdb=" OG1 THR B 589 "
     model   vdw
     2.602 3.040
  nonbonded pdb=" N   ALA B 356 "
            pdb=" N   LEU B 357 "
     model   vdw
     2.606 2.560
  nonbonded pdb=" N   ALA A 356 "
            pdb=" N   LEU A 357 "
     model   vdw
     2.607 2.560
  nonbonded pdb=" N   GLY A 270 "
            pdb=" O   HIS A 291 "
     model   vdw
     2.610 3.120
  nonbonded pdb=" N   GLY B 270 "
            pdb=" O   HIS B 291 "
     model   vdw
     2.611 3.120
  ... (remaining 67056 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 7 through 106 or resid 109 through 591 or resid 1000))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.050
  Set scattering table:                    0.100
  Process input model:                     24.280
  Find NCS groups from input model:        0.360
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
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      :  0.008   0.074   9223  Z= 0.497
  Angle     :  1.383   6.790  12611  Z= 0.934
  Chirality :  0.084   0.291   1412
  Planarity :  0.010   0.216   1657
  Dihedral  : 18.216  79.266   3383
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.71 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 12.18 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.19), residues: 1146
  helix: -4.02 (0.14), residues: 436
  sheet:  0.01 (0.35), residues: 178
  loop : -2.44 (0.21), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 284 
 HIS   0.008   0.001   HIS B 335 
 PHE   0.014   0.002   PHE A 145 
 TYR   0.017   0.002   TYR A 588 
 ARG   0.006   0.001   ARG A 141 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8239 (mm) cc_final: 0.7799 (mm)
REVERT: A   45 ASP cc_start: 0.8033 (t70) cc_final: 0.7510 (t0)
REVERT: A  222 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8065 (pmm150)
REVERT: A  444 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8187 (tp30)
REVERT: A  476 LYS cc_start: 0.7886 (mttt) cc_final: 0.7002 (mttp)
REVERT: A  479 TYR cc_start: 0.8608 (m-80) cc_final: 0.7193 (m-80)
REVERT: A  489 GLU cc_start: 0.9119 (tt0) cc_final: 0.8716 (tp30)
REVERT: A  522 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8374 (tm-30)
REVERT: A  526 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7124 (t80)
REVERT: A  588 TYR cc_start: 0.7104 (m-80) cc_final: 0.6670 (m-80)
REVERT: B   24 CYS cc_start: 0.8689 (p) cc_final: 0.8338 (p)
REVERT: B  381 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8509 (mp0)
REVERT: B  477 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7820 (ptp90)
REVERT: B  512 LEU cc_start: 0.8810 (mt) cc_final: 0.8524 (tp)
REVERT: B  524 ARG cc_start: 0.9127 (mtt180) cc_final: 0.8757 (tpp-160)
REVERT: B  526 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7776 (t80)
  outliers start: 32
  outliers final: 5
  residues processed: 150
  average time/residue: 0.2453
  time to fit residues: 48.9938
Evaluate side-chains
  79 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  444 GLU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  526 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   chunk 58 optimal weight:    7.9990
   chunk 46 optimal weight:    0.5980
   chunk 89 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 103 optimal weight:    0.0770
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
B  72 GLN
B 290 HIS
B 525 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.125895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.096910 restraints weight = 20451.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.098434 restraints weight = 12545.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.098873 restraints weight = 10107.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9223  Z= 0.201
  Angle     :  0.657   8.891  12611  Z= 0.334
  Chirality :  0.042   0.133   1412
  Planarity :  0.004   0.030   1657
  Dihedral  :  7.365  67.324   1322
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.01 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 17.24 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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: -2.36 (0.22), residues: 1146
  helix: -2.21 (0.20), residues: 450
  sheet:  0.70 (0.39), residues: 164
  loop : -1.62 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 523 
 HIS   0.011   0.001   HIS A  47 
 PHE   0.014   0.002   PHE B 528 
 TYR   0.017   0.002   TYR B 263 
 ARG   0.007   0.001   ARG A 566 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.8042 (ptp) cc_final: 0.7823 (ptt)
REVERT: A  476 LYS cc_start: 0.8178 (mttt) cc_final: 0.7394 (mttp)
REVERT: A  479 TYR cc_start: 0.8108 (m-80) cc_final: 0.7560 (m-80)
REVERT: A  526 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.6137 (t80)
REVERT: A  588 TYR cc_start: 0.7049 (m-80) cc_final: 0.6411 (m-80)
REVERT: B  256 THR cc_start: 0.8719 (m) cc_final: 0.8346 (p)
REVERT: B  340 LEU cc_start: 0.8579 (tp) cc_final: 0.8339 (pp)
REVERT: B  526 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7787 (t80)
  outliers start: 17
  outliers final: 5
  residues processed: 89
  average time/residue: 0.2600
  time to fit residues: 33.8497
Evaluate side-chains
  69 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  588 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 76 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  38 HIS
A 290 HIS
A 291 HIS
A 317 GLN
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 291 HIS
B 532 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.121841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.089215 restraints weight = 21159.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.090609 restraints weight = 12061.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.091226 restraints weight = 7925.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9223  Z= 0.343
  Angle     :  0.663   9.115  12611  Z= 0.333
  Chirality :  0.044   0.144   1412
  Planarity :  0.005   0.051   1657
  Dihedral  :  6.704  64.331   1309
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.97 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.27 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.23), residues: 1146
  helix: -1.26 (0.21), residues: 448
  sheet:  0.80 (0.40), residues: 165
  loop : -1.29 (0.25), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 523 
 HIS   0.007   0.001   HIS B  38 
 PHE   0.010   0.002   PHE A 198 
 TYR   0.027   0.002   TYR B 176 
 ARG   0.006   0.001   ARG A 310 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  476 LYS cc_start: 0.8119 (mttt) cc_final: 0.7626 (mttp)
REVERT: A  479 TYR cc_start: 0.8166 (m-80) cc_final: 0.7912 (m-80)
REVERT: A  512 LEU cc_start: 0.8150 (mp) cc_final: 0.7879 (tp)
REVERT: A  526 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6503 (t80)
REVERT: A  588 TYR cc_start: 0.6921 (m-80) cc_final: 0.6368 (m-80)
REVERT: B  526 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7627 (t80)
  outliers start: 25
  outliers final: 11
  residues processed: 86
  average time/residue: 0.2560
  time to fit residues: 31.3564
Evaluate side-chains
  74 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  588 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 13 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 103 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.118271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.084387 restraints weight = 21066.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.085949 restraints weight = 12436.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.087187 restraints weight = 8669.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   9223  Z= 0.362
  Angle     :  0.664   9.030  12611  Z= 0.330
  Chirality :  0.045   0.137   1412
  Planarity :  0.005   0.060   1657
  Dihedral  :  6.708  65.828   1309
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.49 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.24), residues: 1146
  helix: -0.71 (0.23), residues: 448
  sheet:  0.60 (0.39), residues: 179
  loop : -1.07 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 434 
 HIS   0.007   0.001   HIS B  38 
 PHE   0.011   0.002   PHE A 544 
 TYR   0.029   0.003   TYR B 176 
 ARG   0.005   0.001   ARG B 222 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 58
  time to evaluate  : 2.028 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7676 (pmm150)
REVERT: A  512 LEU cc_start: 0.8140 (mp) cc_final: 0.7919 (tp)
REVERT: A  526 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6244 (t80)
REVERT: A  588 TYR cc_start: 0.7046 (m-80) cc_final: 0.6401 (m-80)
REVERT: B  189 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7375 (tt0)
REVERT: B  523 TRP cc_start: 0.8032 (t60) cc_final: 0.7747 (t60)
REVERT: B  524 ARG cc_start: 0.8409 (mpt180) cc_final: 0.8074 (mmt180)
REVERT: B  526 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7730 (t80)
  outliers start: 33
  outliers final: 17
  residues processed: 86
  average time/residue: 0.2937
  time to fit residues: 37.9319
Evaluate side-chains
  79 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  588 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 57 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 109 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 101 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.123036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.092476 restraints weight = 20726.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.093121 restraints weight = 11502.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.093733 restraints weight = 8934.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9223  Z= 0.185
  Angle     :  0.569   9.626  12611  Z= 0.278
  Chirality :  0.041   0.124   1412
  Planarity :  0.004   0.042   1657
  Dihedral  :  6.282  66.292   1309
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.56 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.24), residues: 1146
  helix: -0.29 (0.23), residues: 451
  sheet:  0.70 (0.39), residues: 185
  loop : -0.82 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.012   0.001   PHE A 544 
 TYR   0.015   0.002   TYR A 479 
 ARG   0.004   0.000   ARG A 310 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6899 (pmm150)
REVERT: A  526 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6213 (t80)
REVERT: A  588 TYR cc_start: 0.6980 (m-80) cc_final: 0.6304 (m-80)
REVERT: B  524 ARG cc_start: 0.8295 (mpt180) cc_final: 0.7971 (mmt-90)
REVERT: B  526 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7835 (t80)
  outliers start: 25
  outliers final: 15
  residues processed: 82
  average time/residue: 0.2260
  time to fit residues: 26.2894
Evaluate side-chains
  74 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue   47 HIS
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  520 ASN
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  588 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 85 optimal weight:    0.0060
   chunk 21 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0070
   chunk 37 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.4214

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

Flipped N/Q/H residues before XYZ refinement:
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.124191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.093012 restraints weight = 20644.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.094692 restraints weight = 11555.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.096073 restraints weight = 7772.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9223  Z= 0.148
  Angle     :  0.554  10.223  12611  Z= 0.267
  Chirality :  0.040   0.161   1412
  Planarity :  0.004   0.040   1657
  Dihedral  :  6.013  66.533   1309
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.21 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.24), residues: 1146
  helix: -0.01 (0.23), residues: 467
  sheet:  0.88 (0.39), residues: 183
  loop : -0.68 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 523 
 HIS   0.003   0.001   HIS B 334 
 PHE   0.017   0.001   PHE A 544 
 TYR   0.017   0.002   TYR A 479 
 ARG   0.004   0.000   ARG A 310 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.6592 (pmm150)
REVERT: B  222 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8000 (pmm150)
REVERT: B  526 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7999 (t80)
REVERT: B  534 MET cc_start: 0.9008 (tpp) cc_final: 0.8619 (tpp)
  outliers start: 23
  outliers final: 13
  residues processed: 80
  average time/residue: 0.2544
  time to fit residues: 30.0201
Evaluate side-chains
  72 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue   47 HIS
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  541 ILE
Chi-restraints excluded: chain B residue  588 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 79 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.121967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.094370 restraints weight = 21012.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.095317 restraints weight = 13556.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.095960 restraints weight = 10835.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9223  Z= 0.248
  Angle     :  0.593  10.507  12611  Z= 0.289
  Chirality :  0.042   0.204   1412
  Planarity :  0.005   0.040   1657
  Dihedral  :  6.003  67.019   1307
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.75 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.24), residues: 1146
  helix:  0.13 (0.23), residues: 461
  sheet:  0.79 (0.39), residues: 183
  loop : -0.67 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 523 
 HIS   0.005   0.001   HIS B  38 
 PHE   0.019   0.001   PHE A 544 
 TYR   0.019   0.002   TYR B 176 
 ARG   0.004   0.000   ARG A 310 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6574 (pmm150)
REVERT: A  411 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8757 (tp)
REVERT: A  588 TYR cc_start: 0.7286 (m-80) cc_final: 0.6761 (t80)
REVERT: B  189 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7536 (tt0)
REVERT: B  526 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.8073 (t80)
REVERT: B  534 MET cc_start: 0.9061 (tpp) cc_final: 0.8663 (tpp)
  outliers start: 25
  outliers final: 19
  residues processed: 78
  average time/residue: 0.2559
  time to fit residues: 28.9405
Evaluate side-chains
  78 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue   29 ILE
Chi-restraints excluded: chain B residue   47 HIS
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  533 HIS
Chi-restraints excluded: chain B residue  541 ILE
Chi-restraints excluded: chain B residue  588 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0870
   chunk 104 optimal weight:    0.9980
   chunk 41 optimal weight:    0.1980
   chunk 110 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 492 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.123533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.096312 restraints weight = 21105.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.097391 restraints weight = 13777.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.097789 restraints weight = 11617.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9223  Z= 0.173
  Angle     :  0.581  11.523  12611  Z= 0.276
  Chirality :  0.041   0.194   1412
  Planarity :  0.004   0.039   1657
  Dihedral  :  5.864  66.688   1307
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.40 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.25), residues: 1146
  helix:  0.43 (0.24), residues: 461
  sheet:  0.88 (0.39), residues: 183
  loop : -0.56 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 523 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.032   0.001   PHE A 570 
 TYR   0.014   0.002   TYR B 176 
 ARG   0.007   0.000   ARG A 514 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6335 (pmm150)
REVERT: A  411 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8719 (tp)
REVERT: A  572 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7448 (tt)
REVERT: A  588 TYR cc_start: 0.7277 (m-80) cc_final: 0.6808 (t80)
REVERT: B  189 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7456 (tt0)
REVERT: B  526 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8092 (t80)
REVERT: B  534 MET cc_start: 0.9128 (tpp) cc_final: 0.8737 (tpp)
  outliers start: 24
  outliers final: 18
  residues processed: 73
  average time/residue: 0.2091
  time to fit residues: 22.0479
Evaluate side-chains
  76 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 53
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue   47 HIS
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  533 HIS
Chi-restraints excluded: chain B residue  541 ILE
Chi-restraints excluded: chain B residue  588 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0470
   chunk 7 optimal weight:    0.9980
   chunk 87 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
A 398 GLN
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.123904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.096777 restraints weight = 20935.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.097931 restraints weight = 13541.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.098481 restraints weight = 10690.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9223  Z= 0.170
  Angle     :  0.565  11.554  12611  Z= 0.270
  Chirality :  0.041   0.177   1412
  Planarity :  0.004   0.041   1657
  Dihedral  :  5.699  66.905   1307
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.83 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.25), residues: 1146
  helix:  0.68 (0.24), residues: 455
  sheet:  0.93 (0.39), residues: 184
  loop : -0.49 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 523 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.022   0.001   PHE A 570 
 TYR   0.014   0.002   TYR B 176 
 ARG   0.004   0.000   ARG A 310 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6278 (pmm150)
REVERT: A  411 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8708 (tp)
REVERT: A  479 TYR cc_start: 0.7811 (m-80) cc_final: 0.7510 (m-80)
REVERT: A  588 TYR cc_start: 0.7181 (m-80) cc_final: 0.6780 (t80)
REVERT: B  189 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7449 (tt0)
REVERT: B  523 TRP cc_start: 0.8020 (t60) cc_final: 0.7441 (t60)
REVERT: B  526 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7907 (t80)
REVERT: B  534 MET cc_start: 0.9138 (tpp) cc_final: 0.8763 (tpp)
REVERT: B  588 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.5382 (t80)
  outliers start: 20
  outliers final: 14
  residues processed: 71
  average time/residue: 0.2181
  time to fit residues: 22.6620
Evaluate side-chains
  73 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue   47 HIS
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  588 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 84 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 86 optimal weight:    0.5980
   chunk 44 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0020
   chunk 22 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.8790

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

Flipped N/Q/H residues before XYZ refinement:
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.123394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.096201 restraints weight = 20854.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.097040 restraints weight = 13666.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.097666 restraints weight = 10908.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9223  Z= 0.200
  Angle     :  0.579  12.271  12611  Z= 0.276
  Chirality :  0.041   0.129   1412
  Planarity :  0.004   0.038   1657
  Dihedral  :  5.716  66.532   1307
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.94 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.25), residues: 1146
  helix:  0.78 (0.24), residues: 455
  sheet:  0.91 (0.39), residues: 183
  loop : -0.48 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 523 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.021   0.001   PHE A 570 
 TYR   0.015   0.002   TYR B 176 
 ARG   0.004   0.000   ARG A 310 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 1.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6333 (pmm150)
REVERT: A  411 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8708 (tp)
REVERT: A  479 TYR cc_start: 0.7829 (m-80) cc_final: 0.7530 (m-80)
REVERT: A  526 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6474 (t80)
REVERT: B  189 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7468 (tt0)
REVERT: B  523 TRP cc_start: 0.8050 (t60) cc_final: 0.7736 (t60)
REVERT: B  526 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7782 (t80)
REVERT: B  534 MET cc_start: 0.9142 (tpp) cc_final: 0.8802 (tpp)
REVERT: B  588 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.5431 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 71
  average time/residue: 0.2408
  time to fit residues: 25.7494
Evaluate side-chains
  74 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue   47 HIS
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  588 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 94 optimal weight:    0.8980
   chunk 109 optimal weight:    0.0270
   chunk 7 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 75 optimal weight:    0.3980
   chunk 10 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0470
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
B 262 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.124722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.097734 restraints weight = 20858.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.098790 restraints weight = 13421.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.099450 restraints weight = 10429.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9223  Z= 0.147
  Angle     :  0.564  11.977  12611  Z= 0.265
  Chirality :  0.040   0.122   1412
  Planarity :  0.004   0.037   1657
  Dihedral  :  5.530  65.247   1307
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.94 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.25), residues: 1146
  helix:  0.97 (0.24), residues: 454
  sheet:  1.06 (0.39), residues: 183
  loop : -0.33 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 523 
 HIS   0.003   0.001   HIS B 586 
 PHE   0.016   0.001   PHE A 570 
 TYR   0.012   0.002   TYR B 176 
 ARG   0.005   0.000   ARG B 514 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3040.93 seconds
wall clock time: 55 minutes 41.17 seconds (3341.17 seconds total)