Starting phenix.real_space_refine
on Sat Dec 28 22:51:27 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avw_15685/12_2024/8avw_15685.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avw_15685/12_2024/8avw_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_15685/12_2024/8avw_15685.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avw_15685/12_2024/8avw_15685.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avw_15685/12_2024/8avw_15685.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avw_15685/12_2024/8avw_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-5532/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: 7.28, per 1000 atoms: 0.81
  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: 2.40
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.99
  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: 2.82

  Time building geometry restraints manager: 2.74 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:             4.450
  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:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.070
  Find NCS groups from input model:        0.390
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.270
-------------------------------------------------------------------------------
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  : 0.847 
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: 0.2627
  time to fit residues: 52.1171
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  : 0.914 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
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  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.8333 (ptp) cc_final: 0.8107 (ptt)
REVERT: A  222 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8190 (pmm150)
REVERT: A  398 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8765 (mm110)
REVERT: A  476 LYS cc_start: 0.7742 (mttt) cc_final: 0.7037 (mttp)
REVERT: A  479 TYR cc_start: 0.8480 (m-80) cc_final: 0.7496 (m-80)
REVERT: A  489 GLU cc_start: 0.9035 (tt0) cc_final: 0.8660 (tp30)
REVERT: A  522 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8301 (tm-30)
REVERT: A  526 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7243 (t80)
REVERT: A  588 TYR cc_start: 0.7134 (m-80) cc_final: 0.6553 (m-80)
REVERT: B   24 CYS cc_start: 0.8604 (p) cc_final: 0.8353 (p)
REVERT: B  256 THR cc_start: 0.8765 (m) cc_final: 0.8323 (p)
REVERT: B  263 TYR cc_start: 0.8110 (t80) cc_final: 0.7821 (t80)
REVERT: B  340 LEU cc_start: 0.8671 (tp) cc_final: 0.8269 (pp)
REVERT: B  469 PHE cc_start: 0.7602 (m-80) cc_final: 0.7279 (m-80)
REVERT: B  526 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7932 (t80)
  outliers start: 17
  outliers final: 5
  residues processed: 89
  average time/residue: 0.2243
  time to fit residues: 28.3183
Evaluate side-chains
  72 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  398 GLN
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 57 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 86 optimal weight:    0.5980
   chunk 70 optimal weight:    0.2980
   chunk 28 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.3184

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9223  Z= 0.269
  Angle     :  0.617   8.960  12611  Z= 0.309
  Chirality :  0.043   0.138   1412
  Planarity :  0.004   0.044   1657
  Dihedral  :  6.644  63.897   1313
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.88 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.62 %
    Favored  : 81.68 %
  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: 451
  sheet:  0.91 (0.41), residues: 165
  loop : -1.32 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 434 
 HIS   0.006   0.001   HIS B  38 
 PHE   0.010   0.001   PHE A 544 
 TYR   0.021   0.002   TYR B 176 
 ARG   0.006   0.000   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
  94 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8753 (mm110)
REVERT: A  476 LYS cc_start: 0.7776 (mttt) cc_final: 0.7253 (mttp)
REVERT: A  479 TYR cc_start: 0.8436 (m-80) cc_final: 0.8214 (m-80)
REVERT: A  489 GLU cc_start: 0.8968 (tt0) cc_final: 0.8629 (tp30)
REVERT: A  512 LEU cc_start: 0.7832 (mp) cc_final: 0.7593 (tp)
REVERT: A  522 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8208 (tm-30)
REVERT: A  526 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7065 (t80)
REVERT: A  588 TYR cc_start: 0.6997 (m-80) cc_final: 0.6428 (m-80)
REVERT: A  591 LEU cc_start: 0.7359 (tt) cc_final: 0.7123 (pp)
REVERT: B   24 CYS cc_start: 0.8580 (p) cc_final: 0.8238 (p)
REVERT: B  120 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7782 (tm-30)
REVERT: B  263 TYR cc_start: 0.8162 (t80) cc_final: 0.7924 (t80)
REVERT: B  340 LEU cc_start: 0.8650 (tp) cc_final: 0.8260 (pp)
REVERT: B  502 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7121 (tt)
REVERT: B  523 TRP cc_start: 0.7878 (t60) cc_final: 0.7459 (t60)
REVERT: B  524 ARG cc_start: 0.8623 (mpt180) cc_final: 0.8378 (mmt180)
REVERT: B  526 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7795 (t80)
  outliers start: 25
  outliers final: 11
  residues processed: 90
  average time/residue: 0.2521
  time to fit residues: 31.8694
Evaluate side-chains
  82 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
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  398 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  120 GLU
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  502 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 102 optimal weight:   10.0000
   chunk 77 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0670
   chunk 98 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.6520

-------------------------------------------------------------------------------
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
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9223  Z= 0.166
  Angle     :  0.553   9.183  12611  Z= 0.272
  Chirality :  0.041   0.128   1412
  Planarity :  0.004   0.042   1657
  Dihedral  :  6.339  63.705   1313
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.49 %
    Favored  : 81.14 %
  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: -0.84 (0.24), residues: 1146
  helix: -0.59 (0.22), residues: 459
  sheet:  1.20 (0.41), residues: 164
  loop : -1.03 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 334 
 PHE   0.010   0.001   PHE A 544 
 TYR   0.017   0.002   TYR B 472 
 ARG   0.004   0.000   ARG A 510 

*********************** 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
  92 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 MET cc_start: 0.8404 (tpp) cc_final: 0.8174 (tmm)
REVERT: A  476 LYS cc_start: 0.7776 (mttt) cc_final: 0.7213 (mttp)
REVERT: A  479 TYR cc_start: 0.8457 (m-80) cc_final: 0.8251 (m-80)
REVERT: A  489 GLU cc_start: 0.8995 (tt0) cc_final: 0.8532 (tp30)
REVERT: A  512 LEU cc_start: 0.7737 (mp) cc_final: 0.7500 (tp)
REVERT: A  522 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8190 (tm-30)
REVERT: A  526 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7147 (t80)
REVERT: A  588 TYR cc_start: 0.7030 (m-80) cc_final: 0.6524 (m-80)
REVERT: A  591 LEU cc_start: 0.7386 (tt) cc_final: 0.7042 (pp)
REVERT: B   24 CYS cc_start: 0.8417 (p) cc_final: 0.8133 (p)
REVERT: B  263 TYR cc_start: 0.8130 (t80) cc_final: 0.7929 (t80)
REVERT: B  340 LEU cc_start: 0.8591 (tp) cc_final: 0.8236 (pp)
REVERT: B  523 TRP cc_start: 0.7931 (t60) cc_final: 0.7522 (t60)
REVERT: B  524 ARG cc_start: 0.8603 (tpt170) cc_final: 0.8374 (mmt180)
REVERT: B  526 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7755 (t80)
  outliers start: 22
  outliers final: 12
  residues processed: 89
  average time/residue: 0.2281
  time to fit residues: 28.5809
Evaluate side-chains
  78 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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  526 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  222 ARG
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    0.0030
   chunk 62 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0770
   chunk 82 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.9352

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9223  Z= 0.208
  Angle     :  0.565   9.635  12611  Z= 0.277
  Chirality :  0.041   0.131   1412
  Planarity :  0.004   0.042   1657
  Dihedral  :  6.245  64.479   1313
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.24 %
    Favored  : 80.60 %
  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: -0.51 (0.24), residues: 1146
  helix: -0.24 (0.23), residues: 459
  sheet:  1.02 (0.40), residues: 172
  loop : -0.82 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 434 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.013   0.001   PHE A 544 
 TYR   0.017   0.002   TYR B 176 
 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
  84 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.8269 (ptp) cc_final: 0.8068 (ptt)
REVERT: A  476 LYS cc_start: 0.7791 (mttt) cc_final: 0.7221 (mttp)
REVERT: A  489 GLU cc_start: 0.8902 (tt0) cc_final: 0.8666 (tm-30)
REVERT: A  512 LEU cc_start: 0.7784 (mp) cc_final: 0.7573 (tp)
REVERT: A  522 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8261 (tm-30)
REVERT: A  526 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7209 (t80)
REVERT: A  588 TYR cc_start: 0.7090 (m-80) cc_final: 0.6625 (m-80)
REVERT: A  591 LEU cc_start: 0.7435 (tt) cc_final: 0.6877 (pp)
REVERT: B   24 CYS cc_start: 0.8457 (p) cc_final: 0.8175 (p)
REVERT: B  516 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7048 (mt)
REVERT: B  523 TRP cc_start: 0.7880 (t60) cc_final: 0.7620 (t60)
REVERT: B  524 ARG cc_start: 0.8592 (tpt170) cc_final: 0.8332 (mmt-90)
REVERT: B  526 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7825 (t80)
REVERT: B  534 MET cc_start: 0.9015 (tpp) cc_final: 0.8778 (tpp)
  outliers start: 20
  outliers final: 13
  residues processed: 81
  average time/residue: 0.2344
  time to fit residues: 27.3219
Evaluate side-chains
  78 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
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  526 TYR
Chi-restraints excluded: chain A residue  581 LEU
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  516 LEU
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 37 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0370
   chunk 51 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.9060

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9223  Z= 0.201
  Angle     :  0.552   9.855  12611  Z= 0.271
  Chirality :  0.041   0.128   1412
  Planarity :  0.004   0.041   1657
  Dihedral  :  6.070  65.183   1313
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.92 %
    Favored  : 80.50 %
  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: -0.19 (0.24), residues: 1146
  helix:  0.10 (0.23), residues: 460
  sheet:  0.87 (0.39), residues: 186
  loop : -0.63 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 434 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.013   0.001   PHE A 570 
 TYR   0.017   0.002   TYR B 176 
 ARG   0.003   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: 24
    poor density    : 62
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
REVERT: A  512 LEU cc_start: 0.7817 (mp) cc_final: 0.7588 (tt)
REVERT: A  522 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8394 (tm-30)
REVERT: A  526 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7216 (t80)
REVERT: A  588 TYR cc_start: 0.7141 (m-80) cc_final: 0.6736 (m-80)
REVERT: A  591 LEU cc_start: 0.7440 (tt) cc_final: 0.6850 (pp)
REVERT: B   24 CYS cc_start: 0.8438 (p) cc_final: 0.8130 (p)
REVERT: B  189 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7577 (tt0)
REVERT: B  524 ARG cc_start: 0.8576 (tpt170) cc_final: 0.8320 (mmt-90)
REVERT: B  526 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7901 (t80)
REVERT: B  534 MET cc_start: 0.9125 (tpp) cc_final: 0.8881 (tpp)
  outliers start: 24
  outliers final: 16
  residues processed: 81
  average time/residue: 0.2303
  time to fit residues: 26.3443
Evaluate side-chains
  77 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
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  526 TYR
Chi-restraints excluded: chain A residue  581 LEU
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 109 optimal weight:    0.0980
   chunk 68 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.8188

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9223  Z= 0.356
  Angle     :  0.649  10.667  12611  Z= 0.320
  Chirality :  0.045   0.182   1412
  Planarity :  0.005   0.042   1657
  Dihedral  :  6.407  67.274   1313
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.13 %
    Favored  : 79.85 %
  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: -0.32 (0.24), residues: 1146
  helix:  0.05 (0.23), residues: 466
  sheet:  0.65 (0.39), residues: 184
  loop : -0.69 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 434 
 HIS   0.006   0.001   HIS B  38 
 PHE   0.022   0.002   PHE A 544 
 TYR   0.026   0.003   TYR B 176 
 ARG   0.004   0.000   ARG A 222 

*********************** 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
  84 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 56
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: A  297 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8389 (tt)
REVERT: A  512 LEU cc_start: 0.7860 (mp) cc_final: 0.7621 (tt)
REVERT: A  522 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8381 (tp30)
REVERT: A  526 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7658 (t80)
REVERT: A  588 TYR cc_start: 0.7223 (m-80) cc_final: 0.6768 (m-80)
REVERT: A  591 LEU cc_start: 0.7488 (tt) cc_final: 0.6965 (pp)
REVERT: B   24 CYS cc_start: 0.8587 (p) cc_final: 0.8243 (p)
REVERT: B  189 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7644 (tt0)
REVERT: B  526 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7984 (t80)
REVERT: B  534 MET cc_start: 0.9108 (tpp) cc_final: 0.8864 (tpp)
  outliers start: 28
  outliers final: 18
  residues processed: 78
  average time/residue: 0.2364
  time to fit residues: 26.1367
Evaluate side-chains
  74 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 52
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
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  297 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue   47 HIS
Chi-restraints excluded: chain B residue   67 THR
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9223  Z= 0.193
  Angle     :  0.570  11.246  12611  Z= 0.278
  Chirality :  0.041   0.194   1412
  Planarity :  0.004   0.040   1657
  Dihedral  :  6.138  66.485   1313
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.00 %
    Favored  : 80.06 %
  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: -0.02 (0.25), residues: 1146
  helix:  0.36 (0.23), residues: 466
  sheet:  0.67 (0.37), residues: 196
  loop : -0.56 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 523 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.018   0.001   PHE A 544 
 TYR   0.024   0.002   TYR B 263 
 ARG   0.004   0.000   ARG A 310 

*********************** 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
  73 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: A  512 LEU cc_start: 0.7936 (mp) cc_final: 0.7716 (tt)
REVERT: A  522 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8467 (tp30)
REVERT: A  591 LEU cc_start: 0.7607 (tt) cc_final: 0.7109 (pp)
REVERT: B   24 CYS cc_start: 0.8522 (p) cc_final: 0.8178 (p)
REVERT: B  189 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7566 (tt0)
REVERT: B  526 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.8080 (t80)
REVERT: B  534 MET cc_start: 0.9161 (tpp) cc_final: 0.8921 (tpp)
  outliers start: 18
  outliers final: 14
  residues processed: 70
  average time/residue: 0.2240
  time to fit residues: 22.3588
Evaluate side-chains
  70 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
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  581 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 102 optimal weight:    7.9990
   chunk 105 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 80 optimal weight:    0.0870
   chunk 31 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 108 optimal weight:    7.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.9162

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9223  Z= 0.210
  Angle     :  0.570  11.596  12611  Z= 0.279
  Chirality :  0.041   0.140   1412
  Planarity :  0.004   0.040   1657
  Dihedral  :  5.934  65.684   1311
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.56 %
    Favored  : 80.06 %
  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:  0.06 (0.25), residues: 1146
  helix:  0.45 (0.24), residues: 461
  sheet:  0.63 (0.36), residues: 196
  loop : -0.50 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 523 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.016   0.001   PHE A 570 
 TYR   0.016   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
  78 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  512 LEU cc_start: 0.7951 (mp) cc_final: 0.7745 (tt)
REVERT: A  522 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8324 (tm-30)
REVERT: A  588 TYR cc_start: 0.7528 (m-80) cc_final: 0.6884 (t80)
REVERT: A  591 LEU cc_start: 0.7465 (tt) cc_final: 0.7152 (tt)
REVERT: B   24 CYS cc_start: 0.8558 (p) cc_final: 0.8202 (p)
REVERT: B  189 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7612 (tt0)
REVERT: B  534 MET cc_start: 0.9157 (tpp) cc_final: 0.8947 (tpp)
  outliers start: 22
  outliers final: 16
  residues processed: 76
  average time/residue: 0.2393
  time to fit residues: 26.2296
Evaluate side-chains
  71 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
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  581 LEU
Chi-restraints excluded: chain B residue   47 HIS
Chi-restraints excluded: chain B residue   67 THR
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  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  588 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 75 optimal weight:    0.6980
   chunk 113 optimal weight:    4.9990
   chunk 104 optimal weight:    0.8980
   chunk 90 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9223  Z= 0.208
  Angle     :  0.573  12.298  12611  Z= 0.278
  Chirality :  0.041   0.129   1412
  Planarity :  0.004   0.040   1657
  Dihedral  :  5.787  65.755   1309
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.00 %
    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:  0.17 (0.25), residues: 1146
  helix:  0.62 (0.24), residues: 455
  sheet:  0.61 (0.36), residues: 196
  loop : -0.47 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 523 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.014   0.001   PHE A 570 
 TYR   0.024   0.002   TYR B 526 
 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  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  512 LEU cc_start: 0.7947 (mp) cc_final: 0.7745 (tt)
REVERT: A  522 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8416 (tm-30)
REVERT: A  588 TYR cc_start: 0.7588 (m-80) cc_final: 0.7075 (t80)
REVERT: A  591 LEU cc_start: 0.7460 (tt) cc_final: 0.6878 (pp)
REVERT: B   24 CYS cc_start: 0.8521 (p) cc_final: 0.8175 (p)
REVERT: B  189 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7614 (tt0)
REVERT: B  588 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5631 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 75
  average time/residue: 0.2210
  time to fit residues: 23.9317
Evaluate side-chains
  71 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
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  316 VAL
Chi-restraints excluded: chain A residue  532 HIS
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue   47 HIS
Chi-restraints excluded: chain B residue   67 THR
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  588 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 93 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4163 r_free = 0.4163 target = 0.123781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.096323 restraints weight = 20825.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.097748 restraints weight = 13202.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.098277 restraints weight = 10435.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
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   0.034   9223  Z= 0.187
  Angle     :  0.584  12.661  12611  Z= 0.278
  Chirality :  0.041   0.127   1412
  Planarity :  0.004   0.040   1657
  Dihedral  :  5.704  65.741   1309
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.64 %
    Favored  : 79.42 %
  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:  0.27 (0.25), residues: 1146
  helix:  0.75 (0.24), residues: 455
  sheet:  0.76 (0.38), residues: 184
  loop : -0.48 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 523 
 HIS   0.005   0.001   HIS B 533 
 PHE   0.012   0.001   PHE A 570 
 TYR   0.021   0.002   TYR B 526 
 ARG   0.005   0.000   ARG A 310 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1978.17 seconds
wall clock time: 37 minutes 21.55 seconds (2241.55 seconds total)