Starting phenix.real_space_refine
on Tue Jul 29 12:19:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oce_20017/07_2025/6oce_20017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oce_20017/07_2025/6oce_20017.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oce_20017/07_2025/6oce_20017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oce_20017/07_2025/6oce_20017.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oce_20017/07_2025/6oce_20017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oce_20017/07_2025/6oce_20017.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    7432      2.51       5
     N    1830      2.21       5
     O    1926      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11228
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 689, 5614
          Classifications: {'peptide': 689}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 38, 'TRANS': 650}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 5614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 689, 5614
          Classifications: {'peptide': 689}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 38, 'TRANS': 650}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 6.85, per 1000 atoms: 0.61
  Number of scatterers: 11228
  At special positions: 0
  Unit cell: (144.9, 120.06, 106.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1926      8.00
     N    1830      7.00
     C    7432      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: 2.79
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2652

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 2 sheets defined
      65.2% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 9
      removed outlier: 3.829A  pdb=" N   LEU A   9 " --> pdb=" O   SER A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 9 through 28
      removed outlier: 4.167A  pdb=" N   VAL A  15 " --> pdb=" O   ALA A  11 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LEU A  28 " --> pdb=" O   VAL A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 37
    Processing helix  chain 'A' and resid 38 through 42
      removed outlier: 4.171A  pdb=" N   TRP A  42 " --> pdb=" O   PHE A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 75
      removed outlier: 3.753A  pdb=" N   SER A  74 " --> pdb=" O   LYS A  71 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   TRP A  75 " --> pdb=" O   PHE A  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 71 through 75'
    Processing helix  chain 'A' and resid 78 through 82
      removed outlier: 3.803A  pdb=" N   MET A  82 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 89
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'A' and resid 102 through 127
      Proline residue:  A 111  - end of helix
      removed outlier: 3.854A  pdb=" N   LEU A 118 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   PHE A 121 " --> pdb=" O   SER A 117 " (cutoff:3.500A)
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 154 through 189
      removed outlier: 3.691A  pdb=" N   HIS A 158 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   ALA A 162 " --> pdb=" O   HIS A 158 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   TYR A 163 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ALA A 164 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   THR A 166 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   THR A 169 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 199
      removed outlier: 4.125A  pdb=" N   PHE A 198 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 224
      removed outlier: 3.760A  pdb=" N   GLU A 218 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   HIS A 219 " --> pdb=" O   GLU A 215 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   PHE A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL A 223 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A 224 " --> pdb=" O   PHE A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 269
      removed outlier: 4.311A  pdb=" N   LEU A 241 " --> pdb=" O   ASN A 237 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   ASP A 243 " --> pdb=" O   ASN A 239 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   LEU A 244 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ASN A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LYS A 261 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   TYR A 262 " --> pdb=" O   TYR A 258 " (cutoff:3.500A)
      Proline residue:  A 266  - end of helix
    Processing helix  chain 'A' and resid 287 through 292
    Processing helix  chain 'A' and resid 296 through 309
      removed outlier: 3.503A  pdb=" N   GLU A 301 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA A 302 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 331
    Processing helix  chain 'A' and resid 363 through 385
      removed outlier: 4.012A  pdb=" N   THR A 368 " --> pdb=" O   PHE A 364 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL A 369 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   VAL A 374 " --> pdb=" O   ARG A 370 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA A 375 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASN A 382 " --> pdb=" O   PHE A 378 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   PHE A 383 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 393
      removed outlier: 3.517A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 421
    Processing helix  chain 'A' and resid 424 through 433
      removed outlier: 4.130A  pdb=" N   LYS A 431 " --> pdb=" O   GLY A 427 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A 432 " --> pdb=" O   ILE A 428 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   PHE A 433 " --> pdb=" O   ALA A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
      removed outlier: 3.724A  pdb=" N   ILE A 440 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY A 449 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 473
      removed outlier: 3.713A  pdb=" N   ARG A 458 " --> pdb=" O   SER A 454 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE A 470 " --> pdb=" O   ILE A 466 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASN A 471 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE A 473 " --> pdb=" O   PHE A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 486
      removed outlier: 3.600A  pdb=" N   ILE A 477 " --> pdb=" O   PHE A 473 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL A 478 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   THR A 479 " --> pdb=" O   GLY A 475 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA A 482 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 520
      removed outlier: 3.532A  pdb=" N   THR A 514 " --> pdb=" O   THR A 510 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET A 517 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 529
      removed outlier: 3.548A  pdb=" N   ALA A 525 " --> pdb=" O   TRP A 521 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   GLU A 527 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ILE A 528 " --> pdb=" O   VAL A 524 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   LEU A 529 " --> pdb=" O   ALA A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 542
      removed outlier: 3.538A  pdb=" N   ILE A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE A 542 " --> pdb=" O   HIS A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 554
      removed outlier: 3.674A  pdb=" N   ALA A 554 " --> pdb=" O   ASP A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 583
      Proline residue:  A 567  - end of helix
      removed outlier: 3.800A  pdb=" N   GLN A 570 " --> pdb=" O   GLU A 566 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   VAL A 581 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL A 582 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 607
      removed outlier: 4.169A  pdb=" N   LEU A 591 " --> pdb=" O   LEU A 587 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   VAL A 592 " --> pdb=" O   PRO A 588 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   PHE A 593 " --> pdb=" O   PHE A 589 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LEU A 596 " --> pdb=" O   VAL A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 639
      removed outlier: 3.563A  pdb=" N   VAL A 623 " --> pdb=" O   PHE A 619 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 630 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A 639 " --> pdb=" O   GLN A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 672
      Proline residue:  A 658  - end of helix
    Processing helix  chain 'A' and resid 673 through 678
      removed outlier: 3.504A  pdb=" N   VAL A 677 " --> pdb=" O   GLU A 673 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG A 678 " --> pdb=" O   PRO A 674 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 673 through 678'
    Processing helix  chain 'A' and resid 681 through 695
      removed outlier: 3.975A  pdb=" N   MET A 685 " --> pdb=" O   LEU A 681 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLU A 695 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 706
      removed outlier: 4.053A  pdb=" N   ASN A 706 " --> pdb=" O   ALA A 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 9
      removed outlier: 3.828A  pdb=" N   LEU B   9 " --> pdb=" O   SER B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 28
      removed outlier: 4.169A  pdb=" N   VAL B  15 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ALA B  18 " --> pdb=" O   ASN B  14 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   LEU B  28 " --> pdb=" O   VAL B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 37
    Processing helix  chain 'B' and resid 38 through 42
      removed outlier: 4.161A  pdb=" N   TRP B  42 " --> pdb=" O   PHE B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 74
      removed outlier: 3.744A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 71 through 74'
    Processing helix  chain 'B' and resid 75 through 80
      removed outlier: 4.398A  pdb=" N   LEU B  80 " --> pdb=" O   MET B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 89
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 102 through 127
      removed outlier: 3.796A  pdb=" N   LYS B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
      removed outlier: 3.728A  pdb=" N   LEU B 118 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   PHE B 121 " --> pdb=" O   SER B 117 " (cutoff:3.500A)
      Proline residue:  B 122  - end of helix
    Processing helix  chain 'B' and resid 154 through 189
      removed outlier: 3.700A  pdb=" N   HIS B 158 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ALA B 162 " --> pdb=" O   HIS B 158 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   TYR B 163 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ALA B 164 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   THR B 169 " --> pdb=" O   VAL B 165 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG B 175 " --> pdb=" O   TYR B 171 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA B 189 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
      removed outlier: 4.110A  pdb=" N   PHE B 198 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 224
      removed outlier: 3.663A  pdb=" N   PHE B 221 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL B 223 " --> pdb=" O   HIS B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 260
      removed outlier: 4.376A  pdb=" N   LEU B 241 " --> pdb=" O   ASN B 237 " (cutoff:3.500A)
      removed outlier: 5.427A  pdb=" N   ASP B 243 " --> pdb=" O   ASN B 239 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   LEU B 244 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ASN B 253 " --> pdb=" O   LYS B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 269
      removed outlier: 4.042A  pdb=" N   LYS B 268 " --> pdb=" O   ARG B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 292
    Processing helix  chain 'B' and resid 295 through 309
      removed outlier: 3.529A  pdb=" N   GLU B 300 " --> pdb=" O   LYS B 296 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLU B 301 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG B 305 " --> pdb=" O   GLU B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 331
    Processing helix  chain 'B' and resid 363 through 385
      removed outlier: 3.989A  pdb=" N   THR B 368 " --> pdb=" O   PHE B 364 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   VAL B 369 " --> pdb=" O   VAL B 365 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL B 374 " --> pdb=" O   ARG B 370 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA B 375 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN B 382 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   PHE B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 393
      removed outlier: 3.535A  pdb=" N   ALA B 390 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 421
    Processing helix  chain 'B' and resid 424 through 433
      removed outlier: 4.136A  pdb=" N   LYS B 431 " --> pdb=" O   GLY B 427 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   VAL B 432 " --> pdb=" O   ILE B 428 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE B 433 " --> pdb=" O   ALA B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 449
      removed outlier: 3.723A  pdb=" N   ILE B 440 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLY B 449 " --> pdb=" O   SER B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 473
      removed outlier: 3.710A  pdb=" N   ARG B 458 " --> pdb=" O   SER B 454 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ALA B 461 " --> pdb=" O   GLU B 457 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   PHE B 470 " --> pdb=" O   ILE B 466 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN B 471 " --> pdb=" O   PHE B 467 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE B 473 " --> pdb=" O   PHE B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 486
      removed outlier: 3.623A  pdb=" N   ILE B 477 " --> pdb=" O   PHE B 473 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   VAL B 478 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   THR B 479 " --> pdb=" O   GLY B 475 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA B 482 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 520
      removed outlier: 3.557A  pdb=" N   THR B 514 " --> pdb=" O   THR B 510 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET B 517 " --> pdb=" O   ILE B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 529
      removed outlier: 3.611A  pdb=" N   ALA B 525 " --> pdb=" O   TRP B 521 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLU B 527 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ILE B 528 " --> pdb=" O   VAL B 524 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   LEU B 529 " --> pdb=" O   ALA B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 542
      removed outlier: 4.025A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 531 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE B 536 " --> pdb=" O   ARG B 532 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   PHE B 542 " --> pdb=" O   HIS B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 554
      removed outlier: 3.682A  pdb=" N   ALA B 554 " --> pdb=" O   ASP B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 583
      Proline residue:  B 567  - end of helix
      removed outlier: 3.772A  pdb=" N   GLN B 570 " --> pdb=" O   GLU B 566 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   VAL B 581 " --> pdb=" O   LEU B 577 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL B 582 " --> pdb=" O   VAL B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 607
      removed outlier: 4.165A  pdb=" N   LEU B 591 " --> pdb=" O   LEU B 587 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   VAL B 592 " --> pdb=" O   PRO B 588 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   PHE B 593 " --> pdb=" O   PHE B 589 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU B 596 " --> pdb=" O   VAL B 592 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE B 606 " --> pdb=" O   ARG B 602 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 639
      removed outlier: 3.553A  pdb=" N   VAL B 623 " --> pdb=" O   PHE B 619 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ILE B 629 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA B 630 " --> pdb=" O   ARG B 626 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE B 639 " --> pdb=" O   GLN B 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 641 through 645
      removed outlier: 3.665A  pdb=" N   THR B 644 " --> pdb=" O   LEU B 641 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LYS B 645 " --> pdb=" O   LEU B 642 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 641 through 645'
    Processing helix  chain 'B' and resid 650 through 672
      Proline residue:  B 658  - end of helix
    Processing helix  chain 'B' and resid 673 through 678
      removed outlier: 3.620A  pdb=" N   VAL B 677 " --> pdb=" O   GLU B 673 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG B 678 " --> pdb=" O   PRO B 674 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 673 through 678'
    Processing helix  chain 'B' and resid 681 through 695
      removed outlier: 3.741A  pdb=" N   MET B 685 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLU B 695 " --> pdb=" O   GLU B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 706
      removed outlier: 4.077A  pdb=" N   ASN B 706 " --> pdb=" O   ALA B 702 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 234
      removed outlier: 4.388A  pdb=" N   GLN A 233 " --> pdb=" O   PHE A 320 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 234
      removed outlier: 4.311A  pdb=" N   GLN B 233 " --> pdb=" O   PHE B 320 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1347 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: 2.98

  Time building geometry restraints manager: 3.36 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1720
        1.29 -     1.42: 3174
        1.42 -     1.55: 6578
        1.55 -     1.68: 2
        1.68 -     1.81: 68
  Bond restraints: 11542
  Sorted by residual:
  bond pdb=" CB  PRO A 111 "
       pdb=" CG  PRO A 111 "
    ideal  model  delta    sigma   weight residual
    1.492  1.155  0.337 5.00e-02 4.00e+02 4.55e+01
  bond pdb=" CB  PRO B 111 "
       pdb=" CG  PRO B 111 "
    ideal  model  delta    sigma   weight residual
    1.492  1.227  0.265 5.00e-02 4.00e+02 2.81e+01
  bond pdb=" CA  PRO A 206 "
       pdb=" C   PRO A 206 "
    ideal  model  delta    sigma   weight residual
    1.514  1.531 -0.016 5.50e-03 3.31e+04 8.73e+00
  bond pdb=" CB  PRO B 498 "
       pdb=" CG  PRO B 498 "
    ideal  model  delta    sigma   weight residual
    1.492  1.589 -0.097 5.00e-02 4.00e+02 3.73e+00
  bond pdb=" CA  HIS B 624 "
       pdb=" CB  HIS B 624 "
    ideal  model  delta    sigma   weight residual
    1.529  1.500  0.029 1.55e-02 4.16e+03 3.50e+00
  ... (remaining 11537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.08: 15569
        3.08 -     6.16: 117
        6.16 -     9.24: 7
        9.24 -    12.33: 2
       12.33 -    15.41: 5
  Bond angle restraints: 15700
  Sorted by residual:
  angle pdb=" N   ASP A 285 "
        pdb=" CA  ASP A 285 "
        pdb=" C   ASP A 285 "
      ideal   model   delta    sigma   weight residual
     111.24  125.95  -14.71 1.29e+00 6.01e-01 1.30e+02
  angle pdb=" CA  PRO A 111 "
        pdb=" N   PRO A 111 "
        pdb=" CD  PRO A 111 "
      ideal   model   delta    sigma   weight residual
     112.00   97.80   14.20 1.40e+00 5.10e-01 1.03e+02
  angle pdb=" CA  PRO B 111 "
        pdb=" N   PRO B 111 "
        pdb=" CD  PRO B 111 "
      ideal   model   delta    sigma   weight residual
     112.00   98.69   13.31 1.40e+00 5.10e-01 9.03e+01
  angle pdb=" N   ASP B 285 "
        pdb=" CA  ASP B 285 "
        pdb=" C   ASP B 285 "
      ideal   model   delta    sigma   weight residual
     111.24  121.76  -10.52 1.29e+00 6.01e-01 6.66e+01
  angle pdb=" N   LYS A 296 "
        pdb=" CA  LYS A 296 "
        pdb=" C   LYS A 296 "
      ideal   model   delta    sigma   weight residual
     108.67   96.97   11.70 1.67e+00 3.59e-01 4.91e+01
  ... (remaining 15695 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.73: 6571
       15.73 -    31.45: 223
       31.45 -    47.18: 36
       47.18 -    62.91: 3
       62.91 -    78.63: 3
  Dihedral angle restraints: 6836
    sinusoidal: 2748
      harmonic: 4088
  Sorted by residual:
  dihedral pdb=" CA  PRO B 498 "
           pdb=" C   PRO B 498 "
           pdb=" N   ARG B 499 "
           pdb=" CA  ARG B 499 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.19  -19.81     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  PRO A 498 "
           pdb=" C   PRO A 498 "
           pdb=" N   ARG A 499 "
           pdb=" CA  ARG A 499 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.82  -16.18     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  ILE B 497 "
           pdb=" C   ILE B 497 "
           pdb=" N   PRO B 498 "
           pdb=" CA  PRO B 498 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.39  -15.61     0      5.00e+00 4.00e-02 9.75e+00
  ... (remaining 6833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1610
       0.066 -    0.131: 154
       0.131 -    0.197: 10
       0.197 -    0.263: 1
       0.263 -    0.328: 1
  Chirality restraints: 1776
  Sorted by residual:
  chirality pdb=" CA  ASP A 285 "
            pdb=" N   ASP A 285 "
            pdb=" C   ASP A 285 "
            pdb=" CB  ASP A 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CA  ASP B 285 "
            pdb=" N   ASP B 285 "
            pdb=" C   ASP B 285 "
            pdb=" CB  ASP B 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  PHE A 593 "
            pdb=" N   PHE A 593 "
            pdb=" C   PHE A 593 "
            pdb=" CB  PHE A 593 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.22e-01
  ... (remaining 1773 not shown)

  Planarity restraints: 1954
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 425 "    0.062 5.00e-02 4.00e+02   9.28e-02 1.38e+01
        pdb=" N   PRO A 426 "   -0.160 5.00e-02 4.00e+02
        pdb=" CA  PRO A 426 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 426 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 425 "   -0.061 5.00e-02 4.00e+02   9.15e-02 1.34e+01
        pdb=" N   PRO B 426 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO B 426 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 426 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 624 "   -0.015 2.00e-02 2.50e+03   1.72e-02 4.43e+00
        pdb=" CG  HIS A 624 "    0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 624 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 624 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 624 "    0.004 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 624 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1951 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 31
        2.47 -     3.08: 8313
        3.08 -     3.69: 15845
        3.69 -     4.29: 22616
        4.29 -     4.90: 36167
  Nonbonded interactions: 82972
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 107 "
            pdb=" CG2 VAL B 110 "
     model   vdw
     1.868 3.460
  nonbonded pdb=" O   LYS A 107 "
            pdb=" CG2 VAL A 110 "
     model   vdw
     1.932 3.460
  nonbonded pdb=" OG  SER A 282 "
            pdb=" OE1 GLU A 283 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OG1 THR B 126 "
            pdb=" OG  SER B 144 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   PRO B 122 "
            pdb=" OG1 THR B 126 "
     model   vdw
     2.241 3.040
  ... (remaining 82967 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
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.400
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6152
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.337  11542  Z= 0.274
  Angle     :  0.732  15.407  15700  Z= 0.460
  Chirality :  0.042   0.328   1776
  Planarity :  0.006   0.093   1954
  Dihedral  :  8.069  78.634   4184
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.37 (0.19), residues: 1370
  helix: -2.24 (0.16), residues: 696
  sheet:  0.34 (1.93), residues: 10
  loop : -3.79 (0.21), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A  42 
 HIS   0.019   0.001   HIS A 624 
 PHE   0.027   0.001   PHE B 593 
 TYR   0.006   0.001   TYR A 464 
 ARG   0.002   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21994 (  464)
  hydrogen bonds       : angle       6.78437 ( 1347)
  covalent geometry    : bond        0.00572 (11542)
  covalent geometry    : angle       0.73199 (15700)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.559 
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: A   37 VAL cc_start: 0.6801 (p) cc_final: 0.6498 (m)
REVERT: A   66 MET cc_start: 0.5095 (ttp) cc_final: 0.4718 (ttt)
REVERT: A   67 ARG cc_start: 0.4430 (mtt90) cc_final: 0.4007 (tmm-80)
REVERT: A   87 LEU cc_start: 0.7561 (mt) cc_final: 0.7173 (mt)
REVERT: A  109 PHE cc_start: 0.7130 (m-80) cc_final: 0.6792 (t80)
REVERT: A  137 HIS cc_start: 0.4665 (m90) cc_final: 0.4337 (m-70)
REVERT: A  167 PHE cc_start: 0.8569 (m-10) cc_final: 0.8271 (t80)
REVERT: A  201 LEU cc_start: 0.8002 (tp) cc_final: 0.7428 (tp)
REVERT: A  202 VAL cc_start: 0.7486 (t) cc_final: 0.7246 (t)
REVERT: A  303 ASP cc_start: 0.7081 (t70) cc_final: 0.6876 (m-30)
REVERT: A  373 ILE cc_start: 0.8455 (mm) cc_final: 0.8233 (tt)
REVERT: A  457 GLU cc_start: 0.8301 (tt0) cc_final: 0.7644 (pt0)
REVERT: A  464 TYR cc_start: 0.7955 (t80) cc_final: 0.7256 (t80)
REVERT: A  514 THR cc_start: 0.8577 (p) cc_final: 0.8261 (t)
REVERT: A  552 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7022 (mp0)
REVERT: A  564 TRP cc_start: 0.6832 (m-10) cc_final: 0.6271 (m-90)
REVERT: A  567 PRO cc_start: 0.8073 (Cg_exo) cc_final: 0.7440 (Cg_endo)
REVERT: A  568 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7563 (mtm180)
REVERT: A  585 LEU cc_start: 0.7966 (mt) cc_final: 0.7688 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.1936
  time to fit residues: 49.7787
Evaluate side-chains
  111 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0040
   chunk 41 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 79 optimal weight:    0.4980
   chunk 123 optimal weight:    2.9990
   overall best weight:    1.0996
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 158 HIS
B 422 GLN
B 538 HIS
B 570 GLN
B 604 GLN
B 607 ASN
B 618 GLN
B 682 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.086468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.072788 restraints weight = 26685.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.074429 restraints weight = 19055.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.075555 restraints weight = 14612.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6290
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11542  Z= 0.148
  Angle     :  0.706   7.872  15700  Z= 0.359
  Chirality :  0.045   0.252   1776
  Planarity :  0.006   0.064   1954
  Dihedral  :  3.876  19.422   1506
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 10.07 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.29 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.27 (0.21), residues: 1370
  helix: -1.15 (0.18), residues: 724
  sheet:  0.30 (1.80), residues: 10
  loop : -3.55 (0.22), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  75 
 HIS   0.006   0.001   HIS B 538 
 PHE   0.021   0.001   PHE B 698 
 TYR   0.010   0.001   TYR A 465 
 ARG   0.003   0.000   ARG B 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05026 (  464)
  hydrogen bonds       : angle       4.44676 ( 1347)
  covalent geometry    : bond        0.00319 (11542)
  covalent geometry    : angle       0.70600 (15700)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   67 ARG cc_start: 0.4314 (mtt90) cc_final: 0.4002 (tmm-80)
REVERT: B   82 MET cc_start: 0.5882 (tpt) cc_final: 0.5639 (tpt)
REVERT: B  249 LYS cc_start: 0.8121 (mttm) cc_final: 0.7672 (tmtt)
REVERT: B  250 LYS cc_start: 0.8459 (pttt) cc_final: 0.8139 (pptt)
REVERT: B  264 ARG cc_start: 0.3524 (mtm180) cc_final: 0.2978 (mtt180)
REVERT: B  303 ASP cc_start: 0.7452 (t70) cc_final: 0.7191 (m-30)
REVERT: B  358 ASN cc_start: 0.8134 (m-40) cc_final: 0.7933 (m110)
REVERT: B  444 MET cc_start: 0.8095 (ptp) cc_final: 0.7754 (ptm)
REVERT: B  457 GLU cc_start: 0.8360 (tt0) cc_final: 0.7185 (tm-30)
REVERT: B  464 TYR cc_start: 0.7934 (t80) cc_final: 0.7234 (t80)
REVERT: B  513 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7674 (mt)
REVERT: B  514 THR cc_start: 0.8507 (p) cc_final: 0.8109 (t)
REVERT: B  516 VAL cc_start: 0.7927 (t) cc_final: 0.7501 (p)
REVERT: B  552 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6872 (mp0)
REVERT: B  564 TRP cc_start: 0.6395 (m-10) cc_final: 0.5964 (m-90)
REVERT: B  585 LEU cc_start: 0.8005 (mt) cc_final: 0.7751 (tp)
REVERT: B  603 HIS cc_start: 0.7794 (t70) cc_final: 0.7560 (t-90)
REVERT: B  631 LEU cc_start: 0.7811 (mm) cc_final: 0.7340 (mm)
REVERT: B  666 LYS cc_start: 0.7302 (mmpt) cc_final: 0.6430 (pttt)
REVERT: B  671 ARG cc_start: 0.6357 (ttt180) cc_final: 0.5985 (tpp-160)
REVERT: B  673 GLU cc_start: 0.8957 (tp30) cc_final: 0.8721 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2095
  time to fit residues: 43.1225
Evaluate side-chains
  105 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0980
   chunk 20 optimal weight:    0.1980
   chunk 76 optimal weight:    0.9990
   chunk 109 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 10 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   overall best weight:    1.1984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 485 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.086395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.072580 restraints weight = 26802.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.074151 restraints weight = 18939.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.075299 restraints weight = 14691.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6300
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11542  Z= 0.121
  Angle     :  0.644   7.248  15700  Z= 0.326
  Chirality :  0.043   0.152   1776
  Planarity :  0.005   0.054   1954
  Dihedral  :  3.970  17.782   1506
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 11.53 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.80 %
    Favored  : 98.04 %
  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: -3.16 (0.21), residues: 1370
  helix: -1.03 (0.18), residues: 746
  sheet: -0.13 (1.61), residues: 10
  loop : -3.60 (0.23), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 620 
 HIS   0.002   0.001   HIS A 710 
 PHE   0.032   0.001   PHE B 109 
 TYR   0.012   0.001   TYR B 598 
 ARG   0.004   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  464)
  hydrogen bonds       : angle       3.95226 ( 1347)
  covalent geometry    : bond        0.00262 (11542)
  covalent geometry    : angle       0.64438 (15700)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  104 THR cc_start: 0.8024 (p) cc_final: 0.7822 (p)
REVERT: B  249 LYS cc_start: 0.8203 (mttm) cc_final: 0.7799 (tmtt)
REVERT: B  264 ARG cc_start: 0.3809 (mtm180) cc_final: 0.3585 (mtt180)
REVERT: B  379 PHE cc_start: 0.7598 (t80) cc_final: 0.7097 (t80)
REVERT: B  421 ILE cc_start: 0.5565 (tt) cc_final: 0.5227 (pt)
REVERT: B  444 MET cc_start: 0.8056 (ptp) cc_final: 0.7767 (ptm)
REVERT: B  457 GLU cc_start: 0.8518 (tt0) cc_final: 0.7304 (tm-30)
REVERT: B  464 TYR cc_start: 0.7821 (t80) cc_final: 0.7234 (t80)
REVERT: B  513 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7497 (tp)
REVERT: B  514 THR cc_start: 0.8425 (p) cc_final: 0.8143 (t)
REVERT: B  564 TRP cc_start: 0.6181 (m-10) cc_final: 0.5750 (m-90)
REVERT: B  581 VAL cc_start: 0.8139 (p) cc_final: 0.7799 (p)
REVERT: B  585 LEU cc_start: 0.8036 (mt) cc_final: 0.7727 (tp)
REVERT: B  604 GLN cc_start: 0.8298 (tp40) cc_final: 0.8074 (tp40)
REVERT: B  631 LEU cc_start: 0.8083 (mm) cc_final: 0.7608 (mm)
REVERT: B  663 TRP cc_start: 0.8356 (t-100) cc_final: 0.7953 (t60)
REVERT: B  666 LYS cc_start: 0.7246 (mmpt) cc_final: 0.6419 (pttt)
REVERT: B  671 ARG cc_start: 0.6366 (ttt180) cc_final: 0.5915 (tpp-160)
  outliers start: 1
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1852
  time to fit residues: 34.0372
Evaluate side-chains
  110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 98 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 97 optimal weight:   20.0000
   chunk 103 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    2.1386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 228 HIS
B 603 HIS
** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.083890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.069488 restraints weight = 27356.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.071079 restraints weight = 19244.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.072363 restraints weight = 14894.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6382
moved from start:          0.5108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11542  Z= 0.127
  Angle     :  0.639   7.070  15700  Z= 0.321
  Chirality :  0.043   0.165   1776
  Planarity :  0.005   0.052   1954
  Dihedral  :  4.107  16.250   1506
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.70 %
    Favored  : 87.30 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.59 %
    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: -2.89 (0.22), residues: 1370
  helix: -0.82 (0.18), residues: 748
  sheet:  0.12 (1.66), residues: 10
  loop : -3.47 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 620 
 HIS   0.005   0.001   HIS B 603 
 PHE   0.028   0.001   PHE A 562 
 TYR   0.019   0.001   TYR A 258 
 ARG   0.006   0.000   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  464)
  hydrogen bonds       : angle       4.02180 ( 1347)
  covalent geometry    : bond        0.00278 (11542)
  covalent geometry    : angle       0.63890 (15700)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  104 THR cc_start: 0.7905 (p) cc_final: 0.7528 (p)
REVERT: B  167 PHE cc_start: 0.8680 (m-10) cc_final: 0.8252 (m-10)
REVERT: B  241 LEU cc_start: 0.8231 (mm) cc_final: 0.7723 (pt)
REVERT: B  249 LYS cc_start: 0.8196 (mttm) cc_final: 0.7794 (tmtt)
REVERT: B  250 LYS cc_start: 0.8086 (pttm) cc_final: 0.7526 (tptp)
REVERT: B  406 PRO cc_start: 0.2826 (Cg_exo) cc_final: 0.2427 (Cg_endo)
REVERT: B  421 ILE cc_start: 0.5605 (tt) cc_final: 0.5234 (pt)
REVERT: B  444 MET cc_start: 0.8289 (ptp) cc_final: 0.7502 (ptp)
REVERT: B  457 GLU cc_start: 0.8534 (tt0) cc_final: 0.7216 (tm-30)
REVERT: B  464 TYR cc_start: 0.7967 (t80) cc_final: 0.7215 (t80)
REVERT: B  513 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7233 (tp)
REVERT: B  514 THR cc_start: 0.8384 (p) cc_final: 0.8163 (t)
REVERT: B  552 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6536 (mp0)
REVERT: B  564 TRP cc_start: 0.6331 (m-10) cc_final: 0.6048 (m-90)
REVERT: B  585 LEU cc_start: 0.7960 (mt) cc_final: 0.7661 (tp)
REVERT: B  604 GLN cc_start: 0.8520 (tp40) cc_final: 0.8157 (tp40)
REVERT: B  631 LEU cc_start: 0.8195 (mm) cc_final: 0.7784 (mm)
REVERT: B  662 PHE cc_start: 0.6871 (t80) cc_final: 0.6517 (t80)
REVERT: B  676 PHE cc_start: 0.8148 (t80) cc_final: 0.7786 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1798
  time to fit residues: 33.6041
Evaluate side-chains
  104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 120 optimal weight:    0.0020
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 40 optimal weight:    0.0980
   chunk 27 optimal weight:    0.1980
   chunk 110 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.3988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 603 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.085161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.071787 restraints weight = 27489.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.073352 restraints weight = 19347.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.074403 restraints weight = 14719.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6322
moved from start:          0.5369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11542  Z= 0.116
  Angle     :  0.629   6.745  15700  Z= 0.311
  Chirality :  0.042   0.157   1776
  Planarity :  0.006   0.091   1954
  Dihedral  :  4.075  18.068   1506
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.68 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.63 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.22), residues: 1370
  helix: -0.83 (0.18), residues: 756
  sheet: -0.08 (1.52), residues: 10
  loop : -3.45 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B  75 
 HIS   0.010   0.001   HIS B 603 
 PHE   0.020   0.001   PHE B 562 
 TYR   0.013   0.001   TYR B 258 
 ARG   0.005   0.000   ARG A 508 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03353 (  464)
  hydrogen bonds       : angle       4.00037 ( 1347)
  covalent geometry    : bond        0.00250 (11542)
  covalent geometry    : angle       0.62914 (15700)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  166 THR cc_start: 0.7866 (p) cc_final: 0.7610 (p)
REVERT: B  241 LEU cc_start: 0.8131 (mm) cc_final: 0.7672 (pt)
REVERT: B  249 LYS cc_start: 0.8245 (mttm) cc_final: 0.7886 (tmtt)
REVERT: B  250 LYS cc_start: 0.8018 (pttm) cc_final: 0.7413 (tptp)
REVERT: B  421 ILE cc_start: 0.5531 (tt) cc_final: 0.5184 (pt)
REVERT: B  444 MET cc_start: 0.8250 (ptp) cc_final: 0.7431 (ptp)
REVERT: B  457 GLU cc_start: 0.8397 (tt0) cc_final: 0.7355 (tm-30)
REVERT: B  464 TYR cc_start: 0.7836 (t80) cc_final: 0.7148 (t80)
REVERT: B  513 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7509 (mt)
REVERT: B  514 THR cc_start: 0.8394 (p) cc_final: 0.8113 (t)
REVERT: B  552 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6515 (mp0)
REVERT: B  581 VAL cc_start: 0.8331 (p) cc_final: 0.7943 (p)
REVERT: B  585 LEU cc_start: 0.7945 (mt) cc_final: 0.7618 (tp)
REVERT: B  604 GLN cc_start: 0.8408 (tp40) cc_final: 0.8034 (tp40)
REVERT: B  631 LEU cc_start: 0.8159 (mm) cc_final: 0.7720 (mm)
REVERT: B  662 PHE cc_start: 0.6812 (t80) cc_final: 0.6512 (t80)
REVERT: B  671 ARG cc_start: 0.6346 (ttt180) cc_final: 0.5699 (tpp-160)
REVERT: B  676 PHE cc_start: 0.8387 (t80) cc_final: 0.8145 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1685
  time to fit residues: 31.0956
Evaluate side-chains
  103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 132 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 129 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0870
   chunk 26 optimal weight:    7.9990
   chunk 27 optimal weight:    0.8980
   chunk 117 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0970
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.4160
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.085328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.070856 restraints weight = 28412.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.072395 restraints weight = 20443.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.073567 restraints weight = 15773.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.5587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11542  Z= 0.115
  Angle     :  0.627  10.040  15700  Z= 0.307
  Chirality :  0.042   0.165   1776
  Planarity :  0.005   0.057   1954
  Dihedral  :  4.046  16.705   1506
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.14 %
    Favored  : 86.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  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: -2.68 (0.22), residues: 1370
  helix: -0.73 (0.18), residues: 766
  sheet:  0.18 (1.55), residues: 10
  loop : -3.31 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 564 
 HIS   0.008   0.001   HIS A 232 
 PHE   0.015   0.001   PHE B 593 
 TYR   0.011   0.001   TYR A 258 
 ARG   0.003   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03218 (  464)
  hydrogen bonds       : angle       4.01354 ( 1347)
  covalent geometry    : bond        0.00259 (11542)
  covalent geometry    : angle       0.62662 (15700)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  104 THR cc_start: 0.8064 (p) cc_final: 0.7620 (p)
REVERT: B  167 PHE cc_start: 0.8172 (m-10) cc_final: 0.7950 (t80)
REVERT: B  241 LEU cc_start: 0.8364 (mm) cc_final: 0.7684 (pt)
REVERT: B  249 LYS cc_start: 0.8222 (mttm) cc_final: 0.7922 (tmtt)
REVERT: B  250 LYS cc_start: 0.8118 (pttm) cc_final: 0.7862 (pptt)
REVERT: B  457 GLU cc_start: 0.8329 (tt0) cc_final: 0.7235 (tm-30)
REVERT: B  464 TYR cc_start: 0.7775 (t80) cc_final: 0.7139 (t80)
REVERT: B  513 ILE cc_start: 0.8090 (mp) cc_final: 0.7719 (mp)
REVERT: B  514 THR cc_start: 0.8377 (p) cc_final: 0.8111 (t)
REVERT: B  552 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6430 (mp0)
REVERT: B  581 VAL cc_start: 0.8360 (p) cc_final: 0.8012 (p)
REVERT: B  585 LEU cc_start: 0.7949 (mt) cc_final: 0.7638 (tp)
REVERT: B  631 LEU cc_start: 0.8242 (mm) cc_final: 0.7780 (mm)
REVERT: B  662 PHE cc_start: 0.6497 (t80) cc_final: 0.6261 (t80)
REVERT: B  671 ARG cc_start: 0.6306 (ttt180) cc_final: 0.5708 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1661
  time to fit residues: 29.7933
Evaluate side-chains
  102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 76 optimal weight:    0.0670
   chunk 7 optimal weight:    0.8980
   chunk 125 optimal weight:    2.9990
   chunk 37 optimal weight:    0.1980
   chunk 11 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 38 optimal weight:   40.0000
   chunk 50 optimal weight:    0.9980
   chunk 69 optimal weight:   20.0000
   overall best weight:    0.4918
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 228 HIS
** B 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.086020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.071918 restraints weight = 27887.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.073598 restraints weight = 19577.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.074816 restraints weight = 14754.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6344
moved from start:          0.5790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  11542  Z= 0.117
  Angle     :  0.625   9.793  15700  Z= 0.308
  Chirality :  0.042   0.167   1776
  Planarity :  0.006   0.055   1954
  Dihedral  :  4.058  16.597   1506
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.41 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  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: -2.73 (0.22), residues: 1370
  helix: -0.81 (0.18), residues: 770
  sheet:  0.04 (1.50), residues: 10
  loop : -3.28 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 564 
 HIS   0.003   0.001   HIS A 225 
 PHE   0.017   0.001   PHE B 593 
 TYR   0.013   0.001   TYR B 258 
 ARG   0.004   0.000   ARG A 678 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02997 (  464)
  hydrogen bonds       : angle       3.95989 ( 1347)
  covalent geometry    : bond        0.00248 (11542)
  covalent geometry    : angle       0.62530 (15700)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  167 PHE cc_start: 0.8170 (m-10) cc_final: 0.7922 (t80)
REVERT: B  241 LEU cc_start: 0.8129 (mm) cc_final: 0.7752 (pt)
REVERT: B  249 LYS cc_start: 0.8322 (mttm) cc_final: 0.8051 (tmtt)
REVERT: B  280 PHE cc_start: 0.5648 (m-80) cc_final: 0.4985 (t80)
REVERT: B  406 PRO cc_start: 0.2529 (Cg_exo) cc_final: 0.2212 (Cg_endo)
REVERT: B  444 MET cc_start: 0.8089 (ptp) cc_final: 0.7271 (ptp)
REVERT: B  457 GLU cc_start: 0.8368 (tt0) cc_final: 0.7268 (tm-30)
REVERT: B  464 TYR cc_start: 0.7794 (t80) cc_final: 0.7203 (t80)
REVERT: B  514 THR cc_start: 0.8338 (p) cc_final: 0.8040 (t)
REVERT: B  552 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6433 (mp0)
REVERT: B  581 VAL cc_start: 0.8361 (p) cc_final: 0.8039 (p)
REVERT: B  585 LEU cc_start: 0.8017 (mt) cc_final: 0.7697 (tp)
REVERT: B  604 GLN cc_start: 0.8576 (tp40) cc_final: 0.8328 (tp40)
REVERT: B  631 LEU cc_start: 0.8105 (mm) cc_final: 0.7749 (mm)
REVERT: B  662 PHE cc_start: 0.6593 (t80) cc_final: 0.6359 (t80)
REVERT: B  671 ARG cc_start: 0.6329 (ttt180) cc_final: 0.5690 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1629
  time to fit residues: 29.7205
Evaluate side-chains
  104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 131 optimal weight:    0.0170
   chunk 118 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0000
   chunk 50 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    0.1980
   overall best weight:    0.4022
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 603 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.086330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.072659 restraints weight = 28040.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.074219 restraints weight = 19737.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.075358 restraints weight = 14905.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6325
moved from start:          0.6005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11542  Z= 0.111
  Angle     :  0.650   9.852  15700  Z= 0.318
  Chirality :  0.042   0.151   1776
  Planarity :  0.005   0.056   1954
  Dihedral  :  3.994  16.250   1506
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.12 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  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: -2.78 (0.22), residues: 1370
  helix: -0.84 (0.18), residues: 770
  sheet: -0.13 (1.41), residues: 10
  loop : -3.32 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 564 
 HIS   0.002   0.001   HIS A 225 
 PHE   0.017   0.001   PHE B 593 
 TYR   0.021   0.001   TYR A  98 
 ARG   0.004   0.000   ARG B 508 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02976 (  464)
  hydrogen bonds       : angle       3.94111 ( 1347)
  covalent geometry    : bond        0.00238 (11542)
  covalent geometry    : angle       0.64981 (15700)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  167 PHE cc_start: 0.8135 (m-10) cc_final: 0.7895 (t80)
REVERT: B  249 LYS cc_start: 0.8255 (mttm) cc_final: 0.7949 (tmtt)
REVERT: B  250 LYS cc_start: 0.8101 (pttm) cc_final: 0.7504 (tptp)
REVERT: B  280 PHE cc_start: 0.5548 (m-80) cc_final: 0.4931 (t80)
REVERT: B  406 PRO cc_start: 0.2057 (Cg_exo) cc_final: 0.1802 (Cg_endo)
REVERT: B  444 MET cc_start: 0.8065 (ptp) cc_final: 0.7756 (ptm)
REVERT: B  457 GLU cc_start: 0.8325 (tt0) cc_final: 0.7244 (tm-30)
REVERT: B  464 TYR cc_start: 0.7785 (t80) cc_final: 0.7223 (t80)
REVERT: B  514 THR cc_start: 0.8536 (p) cc_final: 0.8271 (t)
REVERT: B  552 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6376 (mp0)
REVERT: B  581 VAL cc_start: 0.8382 (p) cc_final: 0.8085 (p)
REVERT: B  585 LEU cc_start: 0.8190 (mt) cc_final: 0.7909 (tp)
REVERT: B  604 GLN cc_start: 0.8574 (tp40) cc_final: 0.8272 (tp40)
REVERT: B  631 LEU cc_start: 0.8067 (mm) cc_final: 0.7686 (mm)
REVERT: B  635 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7535 (mp10)
REVERT: B  662 PHE cc_start: 0.6613 (t80) cc_final: 0.6295 (t80)
REVERT: B  666 LYS cc_start: 0.7556 (mmmt) cc_final: 0.6699 (pttt)
REVERT: B  671 ARG cc_start: 0.6266 (ttt180) cc_final: 0.5936 (tpt170)
REVERT: B  673 GLU cc_start: 0.8723 (tp30) cc_final: 0.8505 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1700
  time to fit residues: 30.1886
Evaluate side-chains
  102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 36 optimal weight:    0.2980
   chunk 117 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   overall best weight:    0.7180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.086382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.072359 restraints weight = 28526.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.073962 restraints weight = 19944.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.075056 restraints weight = 14992.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6319
moved from start:          0.6053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11542  Z= 0.111
  Angle     :  0.659   9.857  15700  Z= 0.318
  Chirality :  0.042   0.180   1776
  Planarity :  0.005   0.055   1954
  Dihedral  :  3.934  15.380   1506
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.68 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -2.68 (0.22), residues: 1370
  helix: -0.79 (0.18), residues: 774
  sheet: -1.47 (1.06), residues: 20
  loop : -3.23 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 564 
 HIS   0.003   0.000   HIS A 225 
 PHE   0.017   0.001   PHE A 676 
 TYR   0.017   0.001   TYR B  98 
 ARG   0.004   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02942 (  464)
  hydrogen bonds       : angle       4.00854 ( 1347)
  covalent geometry    : bond        0.00238 (11542)
  covalent geometry    : angle       0.65943 (15700)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  167 PHE cc_start: 0.8118 (m-10) cc_final: 0.7892 (t80)
REVERT: B  249 LYS cc_start: 0.8174 (mttm) cc_final: 0.7930 (tmtt)
REVERT: B  250 LYS cc_start: 0.8046 (pttm) cc_final: 0.7469 (tptp)
REVERT: B  280 PHE cc_start: 0.5578 (m-80) cc_final: 0.4978 (t80)
REVERT: B  406 PRO cc_start: 0.2360 (Cg_exo) cc_final: 0.2154 (Cg_endo)
REVERT: B  444 MET cc_start: 0.8149 (ptp) cc_final: 0.7840 (ptm)
REVERT: B  457 GLU cc_start: 0.8275 (tt0) cc_final: 0.7186 (tm-30)
REVERT: B  464 TYR cc_start: 0.7749 (t80) cc_final: 0.7222 (t80)
REVERT: B  552 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6572 (mp0)
REVERT: B  581 VAL cc_start: 0.8355 (p) cc_final: 0.8039 (p)
REVERT: B  585 LEU cc_start: 0.8125 (mt) cc_final: 0.7872 (tp)
REVERT: B  631 LEU cc_start: 0.8066 (mm) cc_final: 0.7710 (mm)
REVERT: B  635 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7460 (mp10)
REVERT: B  662 PHE cc_start: 0.6717 (t80) cc_final: 0.6312 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1727
  time to fit residues: 30.1740
Evaluate side-chains
  101 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 109 optimal weight:    0.0010
   chunk 11 optimal weight:    0.0370
   chunk 19 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0370
   chunk 46 optimal weight:    0.0570
   chunk 67 optimal weight:    0.2980
   chunk 84 optimal weight:    0.0170
   chunk 53 optimal weight:    0.0070
   overall best weight:    0.0198
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.087460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.073803 restraints weight = 28937.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.075399 restraints weight = 20362.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.076548 restraints weight = 15369.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6291
moved from start:          0.6218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11542  Z= 0.116
  Angle     :  0.668  10.025  15700  Z= 0.322
  Chirality :  0.043   0.202   1776
  Planarity :  0.005   0.054   1954
  Dihedral  :  3.929  14.450   1506
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.12 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.22), residues: 1370
  helix: -0.78 (0.18), residues: 784
  sheet: -1.54 (1.00), residues: 20
  loop : -3.32 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 564 
 HIS   0.010   0.001   HIS A 232 
 PHE   0.021   0.001   PHE A 364 
 TYR   0.017   0.001   TYR B  98 
 ARG   0.003   0.000   ARG B 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02846 (  464)
  hydrogen bonds       : angle       3.92490 ( 1347)
  covalent geometry    : bond        0.00246 (11542)
  covalent geometry    : angle       0.66823 (15700)

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  249 LYS cc_start: 0.8281 (mttm) cc_final: 0.8062 (tptp)
REVERT: B  251 LEU cc_start: 0.6605 (mt) cc_final: 0.6391 (pp)
REVERT: B  280 PHE cc_start: 0.5387 (m-80) cc_final: 0.4881 (t80)
REVERT: B  406 PRO cc_start: 0.2640 (Cg_exo) cc_final: 0.2405 (Cg_endo)
REVERT: B  444 MET cc_start: 0.8170 (ptp) cc_final: 0.7860 (ptm)
REVERT: B  457 GLU cc_start: 0.8366 (tt0) cc_final: 0.7198 (tm-30)
REVERT: B  464 TYR cc_start: 0.7886 (t80) cc_final: 0.7413 (t80)
REVERT: B  552 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6511 (mp0)
REVERT: B  581 VAL cc_start: 0.8313 (p) cc_final: 0.7946 (p)
REVERT: B  585 LEU cc_start: 0.8110 (mt) cc_final: 0.7848 (tp)
REVERT: B  603 HIS cc_start: 0.7898 (t70) cc_final: 0.7601 (t-90)
REVERT: B  604 GLN cc_start: 0.7596 (tp40) cc_final: 0.7234 (tp40)
REVERT: B  631 LEU cc_start: 0.8036 (mm) cc_final: 0.7689 (mm)
REVERT: B  635 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7873 (mp10)
REVERT: B  650 THR cc_start: 0.7654 (p) cc_final: 0.7310 (p)
REVERT: B  676 PHE cc_start: 0.7928 (t80) cc_final: 0.7721 (t80)
REVERT: B  709 LEU cc_start: 0.7452 (mt) cc_final: 0.7179 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1637
  time to fit residues: 29.5482
Evaluate side-chains
  99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0980
   chunk 59 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0980
   chunk 13 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 125 optimal weight:    0.0980
   chunk 33 optimal weight:    4.9990
   chunk 120 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0050
   overall best weight:    0.6596
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 334 GLN
B 603 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.085209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.071453 restraints weight = 28233.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.073061 restraints weight = 19730.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.074214 restraints weight = 14866.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6320
moved from start:          0.6414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11542  Z= 0.112
  Angle     :  0.666   9.817  15700  Z= 0.322
  Chirality :  0.043   0.221   1776
  Planarity :  0.005   0.055   1954
  Dihedral  :  3.891  14.367   1506
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.39 %
    Favored  : 88.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -2.66 (0.22), residues: 1370
  helix: -0.71 (0.18), residues: 768
  sheet: -1.55 (1.00), residues: 20
  loop : -3.31 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 564 
 HIS   0.002   0.001   HIS A 225 
 PHE   0.019   0.001   PHE B 562 
 TYR   0.015   0.001   TYR B  98 
 ARG   0.003   0.000   ARG B 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02910 (  464)
  hydrogen bonds       : angle       3.89954 ( 1347)
  covalent geometry    : bond        0.00242 (11542)
  covalent geometry    : angle       0.66569 (15700)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2593.36 seconds
wall clock time: 46 minutes 52.34 seconds (2812.34 seconds total)