Starting phenix.real_space_refine
on Wed Apr 30 12:53:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e0h_8948/04_2025/6e0h_8948_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e0h_8948/04_2025/6e0h_8948.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6e0h_8948/04_2025/6e0h_8948.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e0h_8948/04_2025/6e0h_8948.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e0h_8948/04_2025/6e0h_8948_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e0h_8948/04_2025/6e0h_8948_neut.cif"
  }
  resolution = 4.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      38      5.16       5
     C    6268      2.51       5
     N    1572      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9524
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 586, 4760
          Classifications: {'peptide': 586}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 27, 'TRANS': 558}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 63
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.58, per 1000 atoms: 0.90
  Number of scatterers: 9524
  At special positions: 0
  Unit cell: (126.051, 75.6309, 99.7451, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      38     16.00
     O    1642      8.00
     N    1572      7.00
     C    6268      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: 2.45
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 2 sheets defined
      70.0% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'B' and resid 27 through 46
      removed outlier: 3.763A  pdb=" N   GLU B  31 " --> pdb=" O   ILE B  27 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE B  36 " --> pdb=" O   ALA B  32 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   VAL B  38 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU B  41 " --> pdb=" O   GLU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 86
      removed outlier: 3.838A  pdb=" N   ARG B  74 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TYR B  77 " --> pdb=" O   LYS B  73 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR B  86 " --> pdb=" O   ARG B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 117
      removed outlier: 3.844A  pdb=" N   ILE B 111 " --> pdb=" O   ARG B 107 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR B 112 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL B 117 " --> pdb=" O   HIS B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 156
      removed outlier: 3.664A  pdb=" N   MET B 152 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ARG B 153 " --> pdb=" O   ARG B 149 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLU B 154 " --> pdb=" O   GLN B 150 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   TRP B 155 " --> pdb=" O   CYS B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 167
    Processing helix  chain 'B' and resid 167 through 172
    Processing helix  chain 'B' and resid 175 through 189
      removed outlier: 3.705A  pdb=" N   TYR B 180 " --> pdb=" O   HIS B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 204
      removed outlier: 3.556A  pdb=" N   PHE B 199 " --> pdb=" O   ALA B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 238
      removed outlier: 3.547A  pdb=" N   VAL B 214 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE B 224 " --> pdb=" O   CYS B 220 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLU B 232 " --> pdb=" O   LYS B 228 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASP B 233 " --> pdb=" O   ARG B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 281
      removed outlier: 3.878A  pdb=" N   MET B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 311
      removed outlier: 3.985A  pdb=" N   ALA B 287 " --> pdb=" O   GLN B 283 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU B 288 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA B 296 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLU B 305 " --> pdb=" O   CYS B 301 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE B 306 " --> pdb=" O   PHE B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 348
      removed outlier: 3.906A  pdb=" N   PHE B 322 " --> pdb=" O   GLY B 318 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ILE B 323 " --> pdb=" O   TYR B 319 " (cutoff:3.500A)
      Proline residue:  B 324  - end of helix
      removed outlier: 3.741A  pdb=" N   ILE B 332 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      Proline residue:  B 333  - end of helix
      removed outlier: 3.809A  pdb=" N   THR B 341 " --> pdb=" O   ALA B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 384
      removed outlier: 4.055A  pdb=" N   LYS B 359 " --> pdb=" O   GLN B 355 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR B 363 " --> pdb=" O   LYS B 359 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   VAL B 369 " --> pdb=" O   LYS B 365 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER B 374 " --> pdb=" O   ASN B 370 " (cutoff:3.500A)
      Proline residue:  B 377  - end of helix
      removed outlier: 4.053A  pdb=" N   THR B 381 " --> pdb=" O   PRO B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 435
      removed outlier: 3.606A  pdb=" N   ILE B 431 " --> pdb=" O   ARG B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 460
      removed outlier: 3.569A  pdb=" N   ILE B 439 " --> pdb=" O   VAL B 435 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   THR B 446 " --> pdb=" O   PHE B 442 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   VAL B 448 " --> pdb=" O   LEU B 444 " (cutoff:3.500A)
      Proline residue:  B 449  - end of helix
      removed outlier: 3.641A  pdb=" N   PHE B 456 " --> pdb=" O   LYS B 452 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TYR B 459 " --> pdb=" O   VAL B 455 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   LYS B 460 " --> pdb=" O   PHE B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 492 through 501
      removed outlier: 3.605A  pdb=" N   ARG B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASN B 499 " --> pdb=" O   THR B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 525
      removed outlier: 3.691A  pdb=" N   ASP B 511 " --> pdb=" O   ASP B 507 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU B 514 " --> pdb=" O   ASP B 510 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   MET B 515 " --> pdb=" O   ASP B 511 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY B 520 " --> pdb=" O   CYS B 516 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   TYR B 521 " --> pdb=" O   ILE B 517 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   LEU B 522 " --> pdb=" O   GLN B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 553
      removed outlier: 3.585A  pdb=" N   SER B 535 " --> pdb=" O   LEU B 531 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL B 542 " --> pdb=" O   ILE B 538 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG B 545 " --> pdb=" O   TRP B 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 591
      removed outlier: 3.580A  pdb=" N   GLY B 574 " --> pdb=" O   LEU B 570 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE B 575 " --> pdb=" O   ASP B 571 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE B 582 " --> pdb=" O   TRP B 578 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   SER B 585 " --> pdb=" O   SER B 581 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL B 588 " --> pdb=" O   SER B 584 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   TYR B 589 " --> pdb=" O   SER B 585 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   PHE B 591 " --> pdb=" O   LEU B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 611 through 635
      removed outlier: 3.844A  pdb=" N   SER B 617 " --> pdb=" O   THR B 613 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ILE B 623 " --> pdb=" O   HIS B 619 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   SER B 630 " --> pdb=" O   TYR B 626 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA B 633 " --> pdb=" O   ARG B 629 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS B 634 " --> pdb=" O   SER B 630 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 635 " --> pdb=" O   ALA B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 659
      removed outlier: 3.729A  pdb=" N   ARG B 653 " --> pdb=" O   MET B 649 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TYR B 654 " --> pdb=" O   MET B 650 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL B 658 " --> pdb=" O   TYR B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 720
    Processing helix  chain 'B' and resid 721 through 724
      removed outlier: 3.991A  pdb=" N   THR B 724 " --> pdb=" O   SER B 721 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 721 through 724'
    Processing helix  chain 'A' and resid 27 through 46
      removed outlier: 3.762A  pdb=" N   GLU A  31 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 86
      removed outlier: 3.839A  pdb=" N   ARG A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 117
      removed outlier: 3.845A  pdb=" N   ILE A 111 " --> pdb=" O   ARG A 107 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TYR A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL A 117 " --> pdb=" O   HIS A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 156
      removed outlier: 3.664A  pdb=" N   MET A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ARG A 153 " --> pdb=" O   ARG A 149 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLU A 154 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   TRP A 155 " --> pdb=" O   CYS A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 175 through 189
      removed outlier: 3.705A  pdb=" N   TYR A 180 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 204
      removed outlier: 3.556A  pdb=" N   PHE A 199 " --> pdb=" O   ALA A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 238
      removed outlier: 3.546A  pdb=" N   VAL A 214 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE A 224 " --> pdb=" O   CYS A 220 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLU A 232 " --> pdb=" O   LYS A 228 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASP A 233 " --> pdb=" O   ARG A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 281
      removed outlier: 3.877A  pdb=" N   MET A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 311
      removed outlier: 3.985A  pdb=" N   ALA A 287 " --> pdb=" O   GLN A 283 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLU A 305 " --> pdb=" O   CYS A 301 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE A 306 " --> pdb=" O   PHE A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 348
      removed outlier: 3.905A  pdb=" N   PHE A 322 " --> pdb=" O   GLY A 318 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ILE A 323 " --> pdb=" O   TYR A 319 " (cutoff:3.500A)
      Proline residue:  A 324  - end of helix
      removed outlier: 3.740A  pdb=" N   ILE A 332 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      Proline residue:  A 333  - end of helix
      removed outlier: 3.809A  pdb=" N   THR A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 384
      removed outlier: 4.056A  pdb=" N   LYS A 359 " --> pdb=" O   GLN A 355 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 363 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER A 374 " --> pdb=" O   ASN A 370 " (cutoff:3.500A)
      Proline residue:  A 377  - end of helix
      removed outlier: 4.053A  pdb=" N   THR A 381 " --> pdb=" O   PRO A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 435
      removed outlier: 3.606A  pdb=" N   ILE A 431 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 460
      removed outlier: 3.569A  pdb=" N   ILE A 439 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   THR A 446 " --> pdb=" O   PHE A 442 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   VAL A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      Proline residue:  A 449  - end of helix
      removed outlier: 3.641A  pdb=" N   PHE A 456 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR A 459 " --> pdb=" O   VAL A 455 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   LYS A 460 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 501
      removed outlier: 3.605A  pdb=" N   ARG A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASN A 499 " --> pdb=" O   THR A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 525
      removed outlier: 3.691A  pdb=" N   ASP A 511 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU A 514 " --> pdb=" O   ASP A 510 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   MET A 515 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLY A 520 " --> pdb=" O   CYS A 516 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   TYR A 521 " --> pdb=" O   ILE A 517 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LEU A 522 " --> pdb=" O   GLN A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 553
      removed outlier: 3.585A  pdb=" N   SER A 535 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A 542 " --> pdb=" O   ILE A 538 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ARG A 545 " --> pdb=" O   TRP A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 591
      removed outlier: 3.579A  pdb=" N   GLY A 574 " --> pdb=" O   LEU A 570 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE A 575 " --> pdb=" O   ASP A 571 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE A 582 " --> pdb=" O   TRP A 578 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER A 585 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A 588 " --> pdb=" O   SER A 584 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TYR A 589 " --> pdb=" O   SER A 585 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A 591 " --> pdb=" O   LEU A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 635
      removed outlier: 3.844A  pdb=" N   SER A 617 " --> pdb=" O   THR A 613 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ILE A 623 " --> pdb=" O   HIS A 619 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   SER A 630 " --> pdb=" O   TYR A 626 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA A 633 " --> pdb=" O   ARG A 629 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS A 634 " --> pdb=" O   SER A 630 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A 635 " --> pdb=" O   ALA A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 659
      removed outlier: 3.730A  pdb=" N   ARG A 653 " --> pdb=" O   MET A 649 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TYR A 654 " --> pdb=" O   MET A 650 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A 658 " --> pdb=" O   TYR A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 720
    Processing helix  chain 'A' and resid 721 through 724
      removed outlier: 3.991A  pdb=" N   THR A 724 " --> pdb=" O   SER A 721 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 721 through 724'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 21
      removed outlier: 8.099A  pdb=" N   TYR B  18 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   ARG B  65 " --> pdb=" O   TYR B  18 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ILE B  20 " --> pdb=" O   PHE B  63 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   PHE B  63 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   VAL B  62 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL B  52 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   VAL B  64 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   THR B  50 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21
      removed outlier: 8.099A  pdb=" N   TYR A  18 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   ARG A  65 " --> pdb=" O   TYR A  18 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   ILE A  20 " --> pdb=" O   PHE A  63 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   PHE A  63 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   VAL A  62 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL A  52 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   VAL A  64 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   THR A  50 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    472 hydrogen bonds defined for protein.
    1416 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: 2.43

  Time building geometry restraints manager: 2.87 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: 2896
        1.34 -     1.46: 2123
        1.46 -     1.57: 4695
        1.57 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 9770
  Sorted by residual:
  bond pdb=" CB  TYR A 352 "
       pdb=" CG  TYR A 352 "
    ideal  model  delta    sigma   weight residual
    1.512  1.455  0.057 2.20e-02 2.07e+03 6.62e+00
  bond pdb=" CB  TYR B 352 "
       pdb=" CG  TYR B 352 "
    ideal  model  delta    sigma   weight residual
    1.512  1.455  0.057 2.20e-02 2.07e+03 6.62e+00
  bond pdb=" N   ALA B 609 "
       pdb=" CA  ALA B 609 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.030 1.31e-02 5.83e+03 5.38e+00
  bond pdb=" N   ALA A 609 "
       pdb=" CA  ALA A 609 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.030 1.31e-02 5.83e+03 5.34e+00
  bond pdb=" CB  TRP A  84 "
       pdb=" CG  TRP A  84 "
    ideal  model  delta    sigma   weight residual
    1.498  1.428  0.070 3.10e-02 1.04e+03 5.15e+00
  ... (remaining 9765 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 12409
        2.08 -     4.15: 693
        4.15 -     6.23: 118
        6.23 -     8.30: 44
        8.30 -    10.38: 12
  Bond angle restraints: 13276
  Sorted by residual:
  angle pdb=" N   SER A 390 "
        pdb=" CA  SER A 390 "
        pdb=" C   SER A 390 "
      ideal   model   delta    sigma   weight residual
     111.28  100.90   10.38 1.09e+00 8.42e-01 9.07e+01
  angle pdb=" N   SER B 390 "
        pdb=" CA  SER B 390 "
        pdb=" C   SER B 390 "
      ideal   model   delta    sigma   weight residual
     111.28  100.94   10.34 1.09e+00 8.42e-01 8.99e+01
  angle pdb=" CA  ALA A 609 "
        pdb=" C   ALA A 609 "
        pdb=" N   LEU A 610 "
      ideal   model   delta    sigma   weight residual
     118.81  124.60   -5.79 1.15e+00 7.56e-01 2.54e+01
  angle pdb=" CA  ALA B 609 "
        pdb=" C   ALA B 609 "
        pdb=" N   LEU B 610 "
      ideal   model   delta    sigma   weight residual
     118.81  124.60   -5.79 1.15e+00 7.56e-01 2.53e+01
  angle pdb=" CA  TYR B 352 "
        pdb=" CB  TYR B 352 "
        pdb=" CG  TYR B 352 "
      ideal   model   delta    sigma   weight residual
     113.90  105.78    8.12 1.80e+00 3.09e-01 2.03e+01
  ... (remaining 13271 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.97: 5204
       13.97 -    27.94: 404
       27.94 -    41.91: 114
       41.91 -    55.88: 16
       55.88 -    69.85: 2
  Dihedral angle restraints: 5740
    sinusoidal: 2266
      harmonic: 3474
  Sorted by residual:
  dihedral pdb=" CA  TRP A 155 "
           pdb=" C   TRP A 155 "
           pdb=" N   SER A 156 "
           pdb=" CA  SER A 156 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  TRP B 155 "
           pdb=" C   TRP B 155 "
           pdb=" N   SER B 156 "
           pdb=" CA  SER B 156 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.59   24.41     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  LYS B 249 "
           pdb=" C   LYS B 249 "
           pdb=" N   ARG B 250 "
           pdb=" CA  ARG B 250 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.36  -22.64     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 5737 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 871
       0.047 -    0.094: 458
       0.094 -    0.141: 138
       0.141 -    0.188: 25
       0.188 -    0.235: 12
  Chirality restraints: 1504
  Sorted by residual:
  chirality pdb=" CA  THR B  29 "
            pdb=" N   THR B  29 "
            pdb=" C   THR B  29 "
            pdb=" CB  THR B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  THR A  29 "
            pdb=" N   THR A  29 "
            pdb=" C   THR A  29 "
            pdb=" CB  THR A  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  SER A 390 "
            pdb=" N   SER A 390 "
            pdb=" C   SER A 390 "
            pdb=" CB  SER A 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1501 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 352 "    0.040 2.00e-02 2.50e+03   2.14e-02 9.14e+00
        pdb=" CG  TYR A 352 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 352 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 352 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 352 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 352 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 352 "    0.022 2.00e-02 2.50e+03
        pdb=" OH  TYR A 352 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 352 "    0.040 2.00e-02 2.50e+03   2.13e-02 9.09e+00
        pdb=" CG  TYR B 352 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 352 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 352 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 352 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 352 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 352 "    0.022 2.00e-02 2.50e+03
        pdb=" OH  TYR B 352 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 376 "    0.045 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO A 377 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 377 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 377 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2596
        2.79 -     3.32: 9281
        3.32 -     3.84: 15371
        3.84 -     4.37: 17589
        4.37 -     4.90: 28764
  Nonbonded interactions: 73601
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 212 "
            pdb=" OG  SER A 526 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OH  TYR B 212 "
            pdb=" OG  SER B 526 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   VAL A 338 "
            pdb=" OG1 THR A 341 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ILE A 582 "
            pdb=" OG  SER A 585 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ILE B 582 "
            pdb=" OG  SER B 585 "
     model   vdw
     2.317 3.040
  ... (remaining 73596 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     26.710
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
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      :  0.009   0.078   9770  Z= 0.397
  Angle     :  1.156  10.379  13276  Z= 0.640
  Chirality :  0.062   0.235   1504
  Planarity :  0.008   0.066   1640
  Dihedral  : 11.245  69.847   3472
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  5.15 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.82 (0.17), residues: 1136
  helix: -3.72 (0.11), residues: 754
  sheet: -3.31 (1.18), residues: 22
  loop : -3.72 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.004   TRP A 155 
 HIS   0.007   0.002   HIS A 619 
 PHE   0.031   0.003   PHE A 388 
 TYR   0.040   0.004   TYR A 352 
 ARG   0.006   0.001   ARG A 651 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30678 (  472)
  hydrogen bonds       : angle      10.38653 ( 1416)
  covalent geometry    : bond        0.00882 ( 9770)
  covalent geometry    : angle       1.15557 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 228
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  334 THR cc_start: 0.8582 (m) cc_final: 0.8259 (p)
REVERT: B  578 TRP cc_start: 0.8629 (t-100) cc_final: 0.8325 (t60)
REVERT: A  151 CYS cc_start: 0.7743 (m) cc_final: 0.7424 (m)
REVERT: A  282 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8957 (tt)
REVERT: A  298 ILE cc_start: 0.9318 (mt) cc_final: 0.9081 (mm)
REVERT: A  499 ASN cc_start: 0.7962 (m110) cc_final: 0.6990 (m-40)
  outliers start: 4
  outliers final: 0
  residues processed: 232
  average time/residue: 0.2711
  time to fit residues: 82.0192
Evaluate side-chains
  104 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 46 optimal weight:    0.2980
   chunk 90 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 185 GLN
B 370 ASN
B 499 ASN
A 185 GLN
A 370 ASN
A 499 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.076419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.066017 restraints weight = 36346.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.067538 restraints weight = 21392.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.068612 restraints weight = 14733.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9770  Z= 0.164
  Angle     :  0.754  10.587  13276  Z= 0.389
  Chirality :  0.044   0.218   1504
  Planarity :  0.006   0.046   1640
  Dihedral  :  5.888  28.005   1284
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  3.47 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.21), residues: 1136
  helix: -1.78 (0.15), residues: 776
  sheet: -2.66 (1.07), residues: 22
  loop : -3.54 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 578 
 HIS   0.002   0.001   HIS A 619 
 PHE   0.019   0.002   PHE B 549 
 TYR   0.045   0.002   TYR B 352 
 ARG   0.006   0.001   ARG A 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05772 (  472)
  hydrogen bonds       : angle       4.70175 ( 1416)
  covalent geometry    : bond        0.00344 ( 9770)
  covalent geometry    : angle       0.75353 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 176
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  151 CYS cc_start: 0.7543 (m) cc_final: 0.7178 (m)
REVERT: B  173 PHE cc_start: 0.8742 (m-80) cc_final: 0.8459 (m-80)
REVERT: B  191 LEU cc_start: 0.9259 (tp) cc_final: 0.8959 (tp)
REVERT: B  297 ILE cc_start: 0.9246 (mm) cc_final: 0.8819 (mm)
REVERT: B  529 TRP cc_start: 0.8445 (t-100) cc_final: 0.8068 (t-100)
REVERT: B  590 MET cc_start: 0.8629 (ptm) cc_final: 0.8151 (ttm)
REVERT: A  151 CYS cc_start: 0.7541 (m) cc_final: 0.7129 (m)
REVERT: A  173 PHE cc_start: 0.8695 (m-80) cc_final: 0.8171 (m-80)
REVERT: A  191 LEU cc_start: 0.9236 (tp) cc_final: 0.8943 (tp)
REVERT: A  297 ILE cc_start: 0.9240 (mm) cc_final: 0.8889 (mm)
REVERT: A  352 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.5983 (m-80)
REVERT: A  354 THR cc_start: 0.7792 (p) cc_final: 0.7234 (m)
REVERT: A  502 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7998 (mt-10)
REVERT: A  506 TYR cc_start: 0.8243 (t80) cc_final: 0.7907 (t80)
REVERT: A  590 MET cc_start: 0.8617 (ptm) cc_final: 0.8124 (ttm)
  outliers start: 3
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1957
  time to fit residues: 50.0957
Evaluate side-chains
  106 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 115 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   chunk 59 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0370
   chunk 63 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    1.2862

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.076108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.065670 restraints weight = 37059.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.067240 restraints weight = 21513.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.068277 restraints weight = 14684.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9770  Z= 0.150
  Angle     :  0.676   7.595  13276  Z= 0.348
  Chirality :  0.043   0.140   1504
  Planarity :  0.005   0.035   1640
  Dihedral  :  5.405  25.580   1284
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.23), residues: 1136
  helix: -0.85 (0.17), residues: 778
  sheet: -2.07 (1.08), residues: 22
  loop : -3.22 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 578 
 HIS   0.002   0.001   HIS A 619 
 PHE   0.012   0.001   PHE A 367 
 TYR   0.024   0.002   TYR B 352 
 ARG   0.004   0.000   ARG A 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04882 (  472)
  hydrogen bonds       : angle       4.29386 ( 1416)
  covalent geometry    : bond        0.00331 ( 9770)
  covalent geometry    : angle       0.67595 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  151 CYS cc_start: 0.7657 (m) cc_final: 0.7261 (m)
REVERT: B  173 PHE cc_start: 0.8732 (m-80) cc_final: 0.8497 (m-80)
REVERT: B  191 LEU cc_start: 0.9342 (tp) cc_final: 0.8972 (tp)
REVERT: B  499 ASN cc_start: 0.7749 (m-40) cc_final: 0.7016 (m-40)
REVERT: B  502 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7548 (mt-10)
REVERT: B  529 TRP cc_start: 0.8405 (t-100) cc_final: 0.7817 (t-100)
REVERT: B  590 MET cc_start: 0.8584 (ptm) cc_final: 0.8187 (ttm)
REVERT: A  151 CYS cc_start: 0.7653 (m) cc_final: 0.7254 (m)
REVERT: A  173 PHE cc_start: 0.8685 (m-80) cc_final: 0.8126 (m-80)
REVERT: A  191 LEU cc_start: 0.9326 (tp) cc_final: 0.9003 (tp)
REVERT: A  499 ASN cc_start: 0.7654 (m-40) cc_final: 0.6783 (m-40)
REVERT: A  502 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8154 (mt-10)
REVERT: A  506 TYR cc_start: 0.8248 (t80) cc_final: 0.7979 (t80)
REVERT: A  570 LEU cc_start: 0.9521 (tp) cc_final: 0.9246 (tt)
REVERT: A  590 MET cc_start: 0.8621 (ptm) cc_final: 0.8169 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2090
  time to fit residues: 41.4413
Evaluate side-chains
  103 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0270
   chunk 40 optimal weight:    6.9990
   chunk 113 optimal weight:    6.9990
   chunk 109 optimal weight:    0.0980
   chunk 2 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.8244

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

Flipped N/Q/H residues before XYZ refinement:
A 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.075331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.065162 restraints weight = 36931.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.066724 restraints weight = 21245.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.067770 restraints weight = 14421.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.4221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9770  Z= 0.168
  Angle     :  0.688   8.058  13276  Z= 0.348
  Chirality :  0.044   0.147   1504
  Planarity :  0.004   0.035   1640
  Dihedral  :  5.143  25.211   1284
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.24), residues: 1136
  helix: -0.35 (0.18), residues: 780
  sheet: -1.88 (1.07), residues: 22
  loop : -3.13 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 578 
 HIS   0.003   0.001   HIS B 619 
 PHE   0.013   0.001   PHE A 367 
 TYR   0.021   0.002   TYR B 375 
 ARG   0.003   0.000   ARG B 276 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04467 (  472)
  hydrogen bonds       : angle       4.14007 ( 1416)
  covalent geometry    : bond        0.00375 ( 9770)
  covalent geometry    : angle       0.68850 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  151 CYS cc_start: 0.7522 (m) cc_final: 0.7130 (m)
REVERT: B  354 THR cc_start: 0.8161 (t) cc_final: 0.7796 (m)
REVERT: B  529 TRP cc_start: 0.8307 (t-100) cc_final: 0.7698 (t-100)
REVERT: B  564 ASP cc_start: 0.8158 (t70) cc_final: 0.7793 (t0)
REVERT: B  590 MET cc_start: 0.8540 (ptm) cc_final: 0.8268 (ttm)
REVERT: A  151 CYS cc_start: 0.7748 (m) cc_final: 0.7346 (m)
REVERT: A  173 PHE cc_start: 0.8731 (m-80) cc_final: 0.8207 (m-80)
REVERT: A  499 ASN cc_start: 0.7611 (m-40) cc_final: 0.6806 (m-40)
REVERT: A  529 TRP cc_start: 0.8018 (t-100) cc_final: 0.7569 (t-100)
REVERT: A  570 LEU cc_start: 0.9518 (tp) cc_final: 0.9252 (tt)
REVERT: A  590 MET cc_start: 0.8541 (ptm) cc_final: 0.8184 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.2121
  time to fit residues: 39.8600
Evaluate side-chains
  94 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 109 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 69 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0770
   chunk 26 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
B 113 HIS
B 499 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.076909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.066529 restraints weight = 36450.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.068103 restraints weight = 20852.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.069184 restraints weight = 14167.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9770  Z= 0.126
  Angle     :  0.664   7.748  13276  Z= 0.328
  Chirality :  0.042   0.144   1504
  Planarity :  0.004   0.035   1640
  Dihedral  :  4.892  23.277   1284
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.24), residues: 1136
  helix:  0.06 (0.18), residues: 778
  sheet: -1.41 (1.23), residues: 18
  loop : -3.04 (0.30), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 578 
 HIS   0.002   0.001   HIS B 113 
 PHE   0.013   0.001   PHE A 190 
 TYR   0.018   0.001   TYR B 352 
 ARG   0.005   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04089 (  472)
  hydrogen bonds       : angle       3.97308 ( 1416)
  covalent geometry    : bond        0.00275 ( 9770)
  covalent geometry    : angle       0.66430 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  150 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8400 (tp-100)
REVERT: B  151 CYS cc_start: 0.7428 (m) cc_final: 0.7050 (m)
REVERT: B  173 PHE cc_start: 0.8732 (m-80) cc_final: 0.8489 (m-80)
REVERT: B  502 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7770 (mt-10)
REVERT: B  529 TRP cc_start: 0.8159 (t-100) cc_final: 0.7357 (t-100)
REVERT: B  564 ASP cc_start: 0.7987 (t70) cc_final: 0.7767 (t0)
REVERT: B  578 TRP cc_start: 0.8154 (t-100) cc_final: 0.7907 (t60)
REVERT: B  590 MET cc_start: 0.8470 (ptm) cc_final: 0.8237 (ttm)
REVERT: A  151 CYS cc_start: 0.7546 (m) cc_final: 0.7231 (m)
REVERT: A  173 PHE cc_start: 0.8683 (m-80) cc_final: 0.8142 (m-80)
REVERT: A  225 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8079 (mm-30)
REVERT: A  499 ASN cc_start: 0.7611 (m-40) cc_final: 0.6747 (m110)
REVERT: A  529 TRP cc_start: 0.7874 (t-100) cc_final: 0.7431 (t-100)
REVERT: A  570 LEU cc_start: 0.9433 (tp) cc_final: 0.9182 (tt)
REVERT: A  590 MET cc_start: 0.8528 (ptm) cc_final: 0.8125 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1973
  time to fit residues: 42.0905
Evaluate side-chains
  101 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 499 ASN
A 113 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.077578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.067295 restraints weight = 36475.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.068881 restraints weight = 20784.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.069964 restraints weight = 14044.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9770  Z= 0.128
  Angle     :  0.671   7.716  13276  Z= 0.332
  Chirality :  0.043   0.148   1504
  Planarity :  0.004   0.034   1640
  Dihedral  :  4.744  22.087   1284
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.24), residues: 1136
  helix:  0.26 (0.18), residues: 774
  sheet: -1.06 (1.28), residues: 18
  loop : -2.94 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 578 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.016   0.001   PHE B 549 
 TYR   0.024   0.001   TYR B 352 
 ARG   0.002   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03953 (  472)
  hydrogen bonds       : angle       3.92902 ( 1416)
  covalent geometry    : bond        0.00286 ( 9770)
  covalent geometry    : angle       0.67101 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  151 CYS cc_start: 0.7785 (m) cc_final: 0.7459 (m)
REVERT: B  173 PHE cc_start: 0.8747 (m-80) cc_final: 0.8437 (m-80)
REVERT: B  354 THR cc_start: 0.7984 (t) cc_final: 0.7677 (m)
REVERT: B  457 ARG cc_start: 0.8842 (ttt180) cc_final: 0.8623 (ptm-80)
REVERT: B  502 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7724 (mt-10)
REVERT: B  529 TRP cc_start: 0.8111 (t-100) cc_final: 0.7485 (t-100)
REVERT: B  590 MET cc_start: 0.8446 (ptm) cc_final: 0.8207 (ttm)
REVERT: A   40 LEU cc_start: 0.9023 (mt) cc_final: 0.8785 (mt)
REVERT: A  151 CYS cc_start: 0.7880 (m) cc_final: 0.7451 (m)
REVERT: A  173 PHE cc_start: 0.8672 (m-80) cc_final: 0.8170 (m-80)
REVERT: A  570 LEU cc_start: 0.9433 (tp) cc_final: 0.9186 (tt)
REVERT: A  590 MET cc_start: 0.8490 (ptm) cc_final: 0.8084 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1819
  time to fit residues: 36.5559
Evaluate side-chains
  95 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   chunk 1 optimal weight:    9.9990
   chunk 103 optimal weight:    0.8980
   chunk 114 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0020
   chunk 40 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
B 113 HIS
B 639 ASN
A 499 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.078364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.068099 restraints weight = 36737.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.069697 restraints weight = 20940.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.070781 restraints weight = 14142.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.4945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9770  Z= 0.126
  Angle     :  0.687   8.174  13276  Z= 0.338
  Chirality :  0.043   0.146   1504
  Planarity :  0.004   0.035   1640
  Dihedral  :  4.671  21.548   1284
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.25), residues: 1136
  helix:  0.31 (0.19), residues: 778
  sheet: -0.89 (1.31), residues: 18
  loop : -2.88 (0.30), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 578 
 HIS   0.002   0.001   HIS B 619 
 PHE   0.013   0.001   PHE B 549 
 TYR   0.018   0.001   TYR B 180 
 ARG   0.004   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  472)
  hydrogen bonds       : angle       4.04978 ( 1416)
  covalent geometry    : bond        0.00277 ( 9770)
  covalent geometry    : angle       0.68667 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  151 CYS cc_start: 0.7949 (m) cc_final: 0.7486 (m)
REVERT: B  173 PHE cc_start: 0.8756 (m-80) cc_final: 0.8380 (m-80)
REVERT: B  502 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7844 (mt-10)
REVERT: B  529 TRP cc_start: 0.8084 (t-100) cc_final: 0.7265 (t-100)
REVERT: B  590 MET cc_start: 0.8502 (ptm) cc_final: 0.8217 (ttm)
REVERT: A  151 CYS cc_start: 0.7843 (m) cc_final: 0.7393 (m)
REVERT: A  173 PHE cc_start: 0.8646 (m-80) cc_final: 0.8383 (m-80)
REVERT: A  352 TYR cc_start: 0.2692 (t80) cc_final: 0.2209 (t80)
REVERT: A  570 LEU cc_start: 0.9418 (tp) cc_final: 0.9174 (tt)
REVERT: A  590 MET cc_start: 0.8488 (ptm) cc_final: 0.8174 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1849
  time to fit residues: 39.0572
Evaluate side-chains
  96 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 11 optimal weight:    0.1980
   chunk 95 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
B 113 HIS
B 518 GLN
B 540 ASN
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
A 709 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.076592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.066206 restraints weight = 37185.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.067765 restraints weight = 21296.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.068844 restraints weight = 14479.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9770  Z= 0.164
  Angle     :  0.705   8.953  13276  Z= 0.350
  Chirality :  0.044   0.178   1504
  Planarity :  0.004   0.032   1640
  Dihedral  :  4.702  21.893   1284
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.25), residues: 1136
  helix:  0.42 (0.19), residues: 776
  sheet: -1.40 (1.20), residues: 18
  loop : -2.76 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 578 
 HIS   0.004   0.001   HIS B 619 
 PHE   0.012   0.001   PHE A 367 
 TYR   0.030   0.002   TYR B 352 
 ARG   0.004   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  472)
  hydrogen bonds       : angle       4.13233 ( 1416)
  covalent geometry    : bond        0.00372 ( 9770)
  covalent geometry    : angle       0.70476 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 GLU cc_start: 0.9272 (mp0) cc_final: 0.9043 (mp0)
REVERT: B  151 CYS cc_start: 0.8172 (m) cc_final: 0.7684 (m)
REVERT: B  173 PHE cc_start: 0.8854 (m-80) cc_final: 0.8553 (m-80)
REVERT: B  354 THR cc_start: 0.8189 (t) cc_final: 0.7853 (m)
REVERT: B  502 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7918 (mt-10)
REVERT: B  529 TRP cc_start: 0.8225 (t-100) cc_final: 0.7477 (t-100)
REVERT: B  590 MET cc_start: 0.8532 (ptm) cc_final: 0.8275 (ttm)
REVERT: A  151 CYS cc_start: 0.8113 (m) cc_final: 0.7559 (m)
REVERT: A  173 PHE cc_start: 0.8772 (m-80) cc_final: 0.8295 (m-80)
REVERT: A  352 TYR cc_start: 0.3072 (t80) cc_final: 0.2636 (t80)
REVERT: A  529 TRP cc_start: 0.7980 (t-100) cc_final: 0.7377 (t-100)
REVERT: A  570 LEU cc_start: 0.9494 (tp) cc_final: 0.9252 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2220
  time to fit residues: 42.8642
Evaluate side-chains
  89 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0870
   chunk 40 optimal weight:    0.0870
   chunk 69 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 108 optimal weight:    0.6980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
B 540 ASN
A 639 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.078792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.068357 restraints weight = 36388.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.069970 restraints weight = 21095.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.071079 restraints weight = 14348.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.5096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9770  Z= 0.127
  Angle     :  0.696   9.203  13276  Z= 0.340
  Chirality :  0.044   0.225   1504
  Planarity :  0.004   0.035   1640
  Dihedral  :  4.665  22.334   1284
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.25), residues: 1136
  helix:  0.35 (0.19), residues: 790
  sheet: -1.27 (1.23), residues: 18
  loop : -2.67 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 578 
 HIS   0.002   0.001   HIS A 619 
 PHE   0.019   0.001   PHE A 549 
 TYR   0.021   0.001   TYR B 352 
 ARG   0.010   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  472)
  hydrogen bonds       : angle       4.05081 ( 1416)
  covalent geometry    : bond        0.00279 ( 9770)
  covalent geometry    : angle       0.69604 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  151 CYS cc_start: 0.7996 (m) cc_final: 0.7461 (m)
REVERT: B  173 PHE cc_start: 0.8747 (m-80) cc_final: 0.8317 (m-80)
REVERT: B  225 GLU cc_start: 0.7955 (mp0) cc_final: 0.7289 (mp0)
REVERT: B  354 THR cc_start: 0.8327 (t) cc_final: 0.7990 (t)
REVERT: B  502 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7853 (mt-10)
REVERT: B  529 TRP cc_start: 0.8049 (t-100) cc_final: 0.7413 (t-100)
REVERT: B  590 MET cc_start: 0.8485 (ptm) cc_final: 0.8218 (ttm)
REVERT: A  151 CYS cc_start: 0.7766 (m) cc_final: 0.7366 (m)
REVERT: A  173 PHE cc_start: 0.8603 (m-80) cc_final: 0.8374 (m-80)
REVERT: A  238 TRP cc_start: 0.8795 (m-10) cc_final: 0.8369 (m-10)
REVERT: A  570 LEU cc_start: 0.9368 (tp) cc_final: 0.9142 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1827
  time to fit residues: 38.4514
Evaluate side-chains
  92 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 7 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0000
   chunk 95 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0970
   chunk 12 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
B 113 HIS
B 619 HIS
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.079512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.069258 restraints weight = 36694.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.070925 restraints weight = 21042.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.071976 restraints weight = 14088.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.5286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9770  Z= 0.131
  Angle     :  0.710   9.746  13276  Z= 0.347
  Chirality :  0.044   0.182   1504
  Planarity :  0.004   0.034   1640
  Dihedral  :  4.605  20.539   1284
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.25), residues: 1136
  helix:  0.37 (0.19), residues: 784
  sheet: -1.24 (1.24), residues: 18
  loop : -2.53 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 578 
 HIS   0.005   0.001   HIS B 619 
 PHE   0.018   0.001   PHE A 549 
 TYR   0.038   0.001   TYR B 352 
 ARG   0.010   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  472)
  hydrogen bonds       : angle       4.13687 ( 1416)
  covalent geometry    : bond        0.00289 ( 9770)
  covalent geometry    : angle       0.71046 (13276)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  151 CYS cc_start: 0.7868 (m) cc_final: 0.7328 (m)
REVERT: B  173 PHE cc_start: 0.8764 (m-80) cc_final: 0.8294 (m-80)
REVERT: B  274 THR cc_start: 0.8799 (p) cc_final: 0.8140 (m)
REVERT: B  354 THR cc_start: 0.8195 (t) cc_final: 0.7884 (m)
REVERT: B  502 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7798 (mt-10)
REVERT: B  506 TYR cc_start: 0.8104 (t80) cc_final: 0.7896 (t80)
REVERT: B  529 TRP cc_start: 0.8019 (t-100) cc_final: 0.7362 (t-100)
REVERT: B  590 MET cc_start: 0.8502 (ptm) cc_final: 0.8240 (ttm)
REVERT: A  151 CYS cc_start: 0.7771 (m) cc_final: 0.7364 (m)
REVERT: A  173 PHE cc_start: 0.8608 (m-80) cc_final: 0.8346 (m-80)
REVERT: A  238 TRP cc_start: 0.8766 (m-10) cc_final: 0.8352 (m-10)
REVERT: A  570 LEU cc_start: 0.9356 (tp) cc_final: 0.9121 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1724
  time to fit residues: 36.7233
Evaluate side-chains
  89 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 66 optimal weight:    0.0870
   chunk 51 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 101 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 85 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 41 optimal weight:    8.9990
   chunk 99 optimal weight:    0.1980
   chunk 26 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0670
   overall best weight:    0.4700

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

Flipped N/Q/H residues before XYZ refinement:
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.079624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.069556 restraints weight = 36115.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.071181 restraints weight = 20807.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.072301 restraints weight = 13965.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.5432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9770  Z= 0.127
  Angle     :  0.698   9.489  13276  Z= 0.340
  Chirality :  0.043   0.183   1504
  Planarity :  0.004   0.034   1640
  Dihedral  :  4.487  20.661   1284
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.25), residues: 1136
  helix:  0.42 (0.19), residues: 786
  sheet: -1.18 (1.24), residues: 18
  loop : -2.51 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP A 578 
 HIS   0.006   0.001   HIS B 619 
 PHE   0.026   0.001   PHE A 199 
 TYR   0.022   0.001   TYR B 352 
 ARG   0.009   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  472)
  hydrogen bonds       : angle       4.05512 ( 1416)
  covalent geometry    : bond        0.00284 ( 9770)
  covalent geometry    : angle       0.69846 (13276)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2894.96 seconds
wall clock time: 51 minutes 47.01 seconds (3107.01 seconds total)