Starting phenix.real_space_refine
on Fri Nov 15 06:52:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwk_35769/11_2024/8iwk_35769.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwk_35769/11_2024/8iwk_35769.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwk_35769/11_2024/8iwk_35769.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwk_35769/11_2024/8iwk_35769.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwk_35769/11_2024/8iwk_35769.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwk_35769/11_2024/8iwk_35769.cif"
  }
  resolution = 3.0
  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=   0.007 sd=   0.143
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      52      5.16       5
     C    5523      2.51       5
     N    1414      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8479
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4230
          Classifications: {'peptide': 545}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 526}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'A8S': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C
  Time building chain proxies: 7.68, per 1000 atoms: 0.91
  Number of scatterers: 8479
  At special positions: 0
  Unit cell: (100.1, 93.5, 122.1, 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      52     16.00
     O    1490      8.00
     N    1414      7.00
     C    5523      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: 2.01
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1996

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      56.9% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 3.677A  pdb=" N   LEU A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 140
      removed outlier: 3.784A  pdb=" N   LEU A 139 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS A 140 " --> pdb=" O   GLN A 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 136 through 140'
    Processing helix  chain 'A' and resid 156 through 169
      removed outlier: 3.600A  pdb=" N   LEU A 167 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 189
      removed outlier: 3.895A  pdb=" N   SER A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 219
      removed outlier: 3.734A  pdb=" N   LYS A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ARG A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 256
      removed outlier: 3.635A  pdb=" N   ARG A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR A 248 " --> pdb=" O   ARG A 244 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 3.683A  pdb=" N   PHE A 275 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 303
      removed outlier: 3.538A  pdb=" N   PHE A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 3.849A  pdb=" N   LEU A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 349
      removed outlier: 3.813A  pdb=" N   THR A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   THR A 347 " --> pdb=" O   THR A 343 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU A 348 " --> pdb=" O   ALA A 344 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 357
      removed outlier: 3.663A  pdb=" N   VAL A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   THR A 355 " --> pdb=" O   PRO A 351 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   CYS A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE A 357 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 397
      removed outlier: 3.563A  pdb=" N   ALA A 384 " --> pdb=" O   THR A 380 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TRP A 386 " --> pdb=" O   CYS A 382 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE A 387 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLN A 389 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   HIS A 395 " --> pdb=" O   CYS A 391 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 3.624A  pdb=" N   GLU A 404 " --> pdb=" O   GLU A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 425
      removed outlier: 3.503A  pdb=" N   PHE A 412 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLN A 413 " --> pdb=" O   LEU A 409 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 410 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   CYS A 421 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 454
      removed outlier: 3.749A  pdb=" N   ARG A 436 " --> pdb=" O   ASP A 432 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY A 438 " --> pdb=" O   HIS A 434 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 462 through 471
      removed outlier: 3.616A  pdb=" N   ALA A 471 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 492
      removed outlier: 3.761A  pdb=" N   MET A 482 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   HIS A 484 " --> pdb=" O   TYR A 480 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   SER A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   MET A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU A 492 " --> pdb=" O   SER A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 505
      removed outlier: 3.639A  pdb=" N   ALA A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   TRP A 505 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 542
      removed outlier: 3.576A  pdb=" N   PHE A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLY A 532 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 549
      removed outlier: 3.694A  pdb=" N   THR A 549 " --> pdb=" O   LYS A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 561
      removed outlier: 3.539A  pdb=" N   THR A 561 " --> pdb=" O   ALA A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 579
      removed outlier: 3.950A  pdb=" N   LYS A 577 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL A 579 " --> pdb=" O   MET A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 594
      removed outlier: 4.035A  pdb=" N   TYR A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA A 591 " --> pdb=" O   ARG A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 658
      removed outlier: 3.748A  pdb=" N   LEU A 642 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE A 643 " --> pdb=" O   VAL A 639 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 644 " --> pdb=" O   GLY A 640 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   TYR A 649 " --> pdb=" O   MET A 645 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ARG A 650 " --> pdb=" O   PHE A 646 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA A 653 " --> pdb=" O   TYR A 649 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 111
      removed outlier: 3.677A  pdb=" N   LEU C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 140
      removed outlier: 3.784A  pdb=" N   LEU C 139 " --> pdb=" O   LYS C 136 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS C 140 " --> pdb=" O   GLN C 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 136 through 140'
    Processing helix  chain 'C' and resid 156 through 169
      removed outlier: 3.601A  pdb=" N   LEU C 167 " --> pdb=" O   PHE C 163 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 189
      removed outlier: 3.896A  pdb=" N   SER C 187 " --> pdb=" O   GLU C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 219
      removed outlier: 3.734A  pdb=" N   LYS C 213 " --> pdb=" O   GLY C 209 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ARG C 214 " --> pdb=" O   GLY C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 256
      removed outlier: 3.635A  pdb=" N   ARG C 244 " --> pdb=" O   THR C 240 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   THR C 248 " --> pdb=" O   ARG C 244 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA C 253 " --> pdb=" O   LEU C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 275
      removed outlier: 3.684A  pdb=" N   PHE C 275 " --> pdb=" O   PHE C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 303
      removed outlier: 3.538A  pdb=" N   PHE C 299 " --> pdb=" O   ALA C 295 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER C 301 " --> pdb=" O   ALA C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 319
      removed outlier: 3.849A  pdb=" N   LEU C 317 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 349
      removed outlier: 3.812A  pdb=" N   THR C 343 " --> pdb=" O   GLN C 339 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   THR C 347 " --> pdb=" O   THR C 343 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU C 348 " --> pdb=" O   ALA C 344 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU C 349 " --> pdb=" O   TYR C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 357
      removed outlier: 3.664A  pdb=" N   VAL C 353 " --> pdb=" O   LEU C 349 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   THR C 355 " --> pdb=" O   PRO C 351 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   CYS C 356 " --> pdb=" O   GLN C 352 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE C 357 " --> pdb=" O   VAL C 353 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 397
      removed outlier: 3.563A  pdb=" N   ALA C 384 " --> pdb=" O   THR C 380 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   TRP C 386 " --> pdb=" O   CYS C 382 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE C 387 " --> pdb=" O   ILE C 383 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER C 388 " --> pdb=" O   ALA C 384 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLN C 389 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   HIS C 395 " --> pdb=" O   CYS C 391 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU C 397 " --> pdb=" O   LEU C 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 404
      removed outlier: 3.623A  pdb=" N   GLU C 404 " --> pdb=" O   GLU C 400 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 425
      removed outlier: 3.503A  pdb=" N   PHE C 412 " --> pdb=" O   LEU C 408 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLN C 413 " --> pdb=" O   LEU C 409 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL C 414 " --> pdb=" O   ARG C 410 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   CYS C 421 " --> pdb=" O   ALA C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 432 through 454
      removed outlier: 3.750A  pdb=" N   ARG C 436 " --> pdb=" O   ASP C 432 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY C 438 " --> pdb=" O   HIS C 434 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER C 444 " --> pdb=" O   LEU C 440 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY C 448 " --> pdb=" O   SER C 444 " (cutoff:3.500A)
      Proline residue:  C 451  - end of helix
    Processing helix  chain 'C' and resid 459 through 461
      No H-bonds generated for 'chain 'C' and resid 459 through 461'
    Processing helix  chain 'C' and resid 462 through 471
      removed outlier: 3.617A  pdb=" N   ALA C 471 " --> pdb=" O   THR C 467 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 492
      removed outlier: 3.761A  pdb=" N   MET C 482 " --> pdb=" O   SER C 478 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   HIS C 484 " --> pdb=" O   TYR C 480 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   SER C 490 " --> pdb=" O   LEU C 486 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   MET C 491 " --> pdb=" O   GLY C 487 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU C 492 " --> pdb=" O   SER C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 493 through 505
      removed outlier: 3.639A  pdb=" N   ALA C 497 " --> pdb=" O   LEU C 493 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   PHE C 502 " --> pdb=" O   SER C 498 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   TRP C 505 " --> pdb=" O   THR C 501 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 512 through 542
      removed outlier: 3.576A  pdb=" N   PHE C 516 " --> pdb=" O   GLY C 512 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU C 518 " --> pdb=" O   VAL C 514 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU C 528 " --> pdb=" O   LEU C 524 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLY C 532 " --> pdb=" O   LEU C 528 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU C 533 " --> pdb=" O   ALA C 529 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY C 534 " --> pdb=" O   SER C 530 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 543 through 549
      removed outlier: 3.694A  pdb=" N   THR C 549 " --> pdb=" O   LYS C 545 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 550 through 561
      removed outlier: 3.539A  pdb=" N   THR C 561 " --> pdb=" O   ALA C 557 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 573 through 579
      removed outlier: 3.949A  pdb=" N   LYS C 577 " --> pdb=" O   VAL C 574 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL C 579 " --> pdb=" O   MET C 576 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 580 through 594
      removed outlier: 4.036A  pdb=" N   TYR C 584 " --> pdb=" O   SER C 580 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA C 591 " --> pdb=" O   ARG C 587 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 635 through 658
      removed outlier: 3.748A  pdb=" N   LEU C 642 " --> pdb=" O   SER C 638 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE C 643 " --> pdb=" O   VAL C 639 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU C 644 " --> pdb=" O   GLY C 640 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   TYR C 649 " --> pdb=" O   MET C 645 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ARG C 650 " --> pdb=" O   PHE C 646 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA C 653 " --> pdb=" O   TYR C 649 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91
    Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 145
      removed outlier: 6.227A  pdb=" N   GLY A 143 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   MET A  97 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY A 290 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   PHE A 288 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 89 through 91
    Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 145
      removed outlier: 6.227A  pdb=" N   GLY C 143 " --> pdb=" O   VAL C 229 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   MET C  97 " --> pdb=" O   THR C 262 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY C 290 " --> pdb=" O   VAL C 278 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   PHE C 288 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    918 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: 2.26

  Time building geometry restraints manager: 2.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1796
        1.33 -     1.45: 1933
        1.45 -     1.57: 4842
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 8655
  Sorted by residual:
  bond pdb=" CB  ARG C 396 "
       pdb=" CG  ARG C 396 "
    ideal  model  delta    sigma   weight residual
    1.520  1.465  0.055 3.00e-02 1.11e+03 3.41e+00
  bond pdb=" CB  ARG A 396 "
       pdb=" CG  ARG A 396 "
    ideal  model  delta    sigma   weight residual
    1.520  1.465  0.055 3.00e-02 1.11e+03 3.38e+00
  bond pdb=" CB  CYS A 421 "
       pdb=" SG  CYS A 421 "
    ideal  model  delta    sigma   weight residual
    1.808  1.749  0.059 3.30e-02 9.18e+02 3.23e+00
  bond pdb=" CB  CYS C 421 "
       pdb=" SG  CYS C 421 "
    ideal  model  delta    sigma   weight residual
    1.808  1.749  0.059 3.30e-02 9.18e+02 3.18e+00
  bond pdb=" CB  ARG A 510 "
       pdb=" CG  ARG A 510 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.80e+00
  ... (remaining 8650 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 11181
        2.30 -     4.61: 451
        4.61 -     6.91: 87
        6.91 -     9.22: 12
        9.22 -    11.52: 4
  Bond angle restraints: 11735
  Sorted by residual:
  angle pdb=" N   ILE A 550 "
        pdb=" CA  ILE A 550 "
        pdb=" C   ILE A 550 "
      ideal   model   delta    sigma   weight residual
     112.96  107.25    5.71 1.00e+00 1.00e+00 3.26e+01
  angle pdb=" N   ILE C 550 "
        pdb=" CA  ILE C 550 "
        pdb=" C   ILE C 550 "
      ideal   model   delta    sigma   weight residual
     112.96  107.29    5.67 1.00e+00 1.00e+00 3.22e+01
  angle pdb=" N   SER A 571 "
        pdb=" CA  SER A 571 "
        pdb=" C   SER A 571 "
      ideal   model   delta    sigma   weight residual
     110.80  118.32   -7.52 2.13e+00 2.20e-01 1.25e+01
  angle pdb=" N   SER C 571 "
        pdb=" CA  SER C 571 "
        pdb=" C   SER C 571 "
      ideal   model   delta    sigma   weight residual
     110.80  118.26   -7.46 2.13e+00 2.20e-01 1.23e+01
  angle pdb=" C   ALA A 350 "
        pdb=" N   PRO A 351 "
        pdb=" CA  PRO A 351 "
      ideal   model   delta    sigma   weight residual
     121.91  117.41    4.50 1.35e+00 5.49e-01 1.11e+01
  ... (remaining 11730 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.04: 4790
       15.04 -    30.09: 256
       30.09 -    45.13: 42
       45.13 -    60.17: 2
       60.17 -    75.22: 6
  Dihedral angle restraints: 5096
    sinusoidal: 1984
      harmonic: 3112
  Sorted by residual:
  dihedral pdb=" CA  PRO C 570 "
           pdb=" C   PRO C 570 "
           pdb=" N   SER C 571 "
           pdb=" CA  SER C 571 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.14   25.86     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  PRO A 570 "
           pdb=" C   PRO A 570 "
           pdb=" N   SER A 571 "
           pdb=" CA  SER A 571 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.19   25.81     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  THR A 202 "
           pdb=" C   THR A 202 "
           pdb=" N   PHE A 203 "
           pdb=" CA  PHE A 203 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.00   20.00     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 5093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1101
       0.073 -    0.146: 256
       0.146 -    0.219: 32
       0.219 -    0.292: 4
       0.292 -    0.365: 2
  Chirality restraints: 1395
  Sorted by residual:
  chirality pdb=" CB  ILE A 134 "
            pdb=" CA  ILE A 134 "
            pdb=" CG1 ILE A 134 "
            pdb=" CG2 ILE A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.37 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CB  ILE C 134 "
            pdb=" CA  ILE C 134 "
            pdb=" CG1 ILE C 134 "
            pdb=" CG2 ILE C 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.30e+00
  chirality pdb=" CB  VAL C 114 "
            pdb=" CA  VAL C 114 "
            pdb=" CG1 VAL C 114 "
            pdb=" CG2 VAL C 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1392 not shown)

  Planarity restraints: 1440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 514 "   -0.046 5.00e-02 4.00e+02   6.79e-02 7.37e+00
        pdb=" N   PRO A 515 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 515 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 515 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 514 "    0.045 5.00e-02 4.00e+02   6.77e-02 7.33e+00
        pdb=" N   PRO C 515 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO C 515 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 515 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 427 "    0.017 2.00e-02 2.50e+03   1.98e-02 5.86e+00
        pdb=" CG  HIS A 427 "   -0.042 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 427 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 427 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 427 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 427 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1437 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2676
        2.83 -     3.35: 7002
        3.35 -     3.87: 12432
        3.87 -     4.38: 14996
        4.38 -     4.90: 26979
  Nonbonded interactions: 64085
  Sorted by model distance:
  nonbonded pdb=" O   SER A 282 "
            pdb=" OG  SER A 282 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   SER C 282 "
            pdb=" OG  SER C 282 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   ILE C 550 "
            pdb=" OG1 THR C 554 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" O   ILE A 550 "
            pdb=" OG1 THR A 554 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   SER C 444 "
            pdb=" OH  TYR C 526 "
     model   vdw
     2.373 3.040
  ... (remaining 64080 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 33 through 662)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.950
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  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:12.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
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      :  0.010   0.083   8655  Z= 0.620
  Angle     :  1.096  11.522  11735  Z= 0.567
  Chirality :  0.063   0.365   1395
  Planarity :  0.007   0.068   1440
  Dihedral  : 10.003  75.217   3100
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.57 (0.15), residues: 1070
  helix: -4.64 (0.08), residues: 610
  sheet: -2.82 (0.47), residues: 96
  loop : -3.81 (0.22), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP A 426 
 HIS   0.022   0.004   HIS A 427 
 PHE   0.031   0.004   PHE A  96 
 TYR   0.026   0.003   TYR A 508 
 ARG   0.006   0.001   ARG A 117 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A  310 MET cc_start: 0.8052 (ptm) cc_final: 0.7574 (ptp)
REVERT: A  599 GLU cc_start: 0.8113 (tt0) cc_final: 0.7419 (pm20)
REVERT: C  117 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7276 (mtp85)
REVERT: C  310 MET cc_start: 0.8199 (ptm) cc_final: 0.7834 (ptp)
REVERT: C  599 GLU cc_start: 0.8065 (tt0) cc_final: 0.7160 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 1.4776
  time to fit residues: 234.0345
Evaluate side-chains
  96 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 531 GLN
C 434 HIS
C 531 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8655  Z= 0.180
  Angle     :  0.619   6.213  11735  Z= 0.317
  Chirality :  0.041   0.149   1395
  Planarity :  0.005   0.048   1440
  Dihedral  :  5.541  33.891   1202
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  :  6.18 %
    Favored  : 91.21 %
  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: -4.61 (0.19), residues: 1070
  helix: -2.81 (0.15), residues: 608
  sheet: -2.78 (0.46), residues: 94
  loop : -3.25 (0.26), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 447 
 HIS   0.005   0.001   HIS C 427 
 PHE   0.017   0.001   PHE A 203 
 TYR   0.016   0.001   TYR C 526 
 ARG   0.007   0.001   ARG C 180 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A  424 MET cc_start: 0.8368 (mmm) cc_final: 0.8029 (mmm)
REVERT: A  576 MET cc_start: 0.7943 (ttt) cc_final: 0.7731 (ttt)
REVERT: A  599 GLU cc_start: 0.8024 (tt0) cc_final: 0.7148 (pm20)
REVERT: C  171 ARG cc_start: 0.7948 (mmm160) cc_final: 0.7737 (mmm160)
REVERT: C  274 MET cc_start: 0.7791 (mtt) cc_final: 0.7545 (mtt)
REVERT: C  424 MET cc_start: 0.8337 (mmm) cc_final: 0.7977 (mmm)
REVERT: C  599 GLU cc_start: 0.7918 (tt0) cc_final: 0.7038 (pm20)
  outliers start: 24
  outliers final: 10
  residues processed: 120
  average time/residue: 1.3330
  time to fit residues: 169.7646
Evaluate side-chains
  105 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  403 HIS
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  545 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0060
   chunk 98 optimal weight:    3.9990
   chunk 106 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 78 optimal weight:    4.9990
   overall best weight:    0.5596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   8655  Z= 0.141
  Angle     :  0.545   5.602  11735  Z= 0.277
  Chirality :  0.039   0.151   1395
  Planarity :  0.004   0.035   1440
  Dihedral  :  4.956  35.053   1202
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  9.54 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (0.23), residues: 1070
  helix: -1.57 (0.19), residues: 604
  sheet: -2.71 (0.45), residues: 92
  loop : -2.71 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 426 
 HIS   0.004   0.001   HIS A 427 
 PHE   0.013   0.001   PHE A 502 
 TYR   0.013   0.001   TYR C 526 
 ARG   0.004   0.000   ARG A 117 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.952 
Fit side-chains
REVERT: C  468 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7648 (ttp-170)
  outliers start: 17
  outliers final: 6
  residues processed: 122
  average time/residue: 1.3031
  time to fit residues: 169.1315
Evaluate side-chains
  108 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  468 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   chunk 50 optimal weight:    4.9990
   chunk 10 optimal weight:    0.3980
   chunk 46 optimal weight:    1.9990
   chunk 65 optimal weight:    0.1980
   chunk 98 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8655  Z= 0.252
  Angle     :  0.620   7.428  11735  Z= 0.312
  Chirality :  0.043   0.154   1395
  Planarity :  0.004   0.038   1440
  Dihedral  :  5.176  33.579   1202
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  :  9.98 %
    Favored  : 87.09 %
  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: -2.87 (0.24), residues: 1070
  helix: -1.28 (0.20), residues: 604
  sheet: -2.71 (0.45), residues: 94
  loop : -2.52 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 426 
 HIS   0.006   0.001   HIS C 219 
 PHE   0.015   0.002   PHE A 502 
 TYR   0.015   0.002   TYR A 526 
 ARG   0.005   0.000   ARG C 180 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A   90 MET cc_start: 0.7492 (ptm) cc_final: 0.7267 (ttt)
REVERT: A  274 MET cc_start: 0.7769 (mtt) cc_final: 0.7565 (mtt)
REVERT: C   97 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8171 (ttt)
REVERT: C  468 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7832 (ttp-170)
  outliers start: 27
  outliers final: 20
  residues processed: 124
  average time/residue: 1.2602
  time to fit residues: 166.3722
Evaluate side-chains
  122 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  403 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  382 CYS
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  468 ARG
Chi-restraints excluded: chain C residue  545 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 1 optimal weight:    9.9990
   chunk 77 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    2.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   8655  Z= 0.446
  Angle     :  0.761   8.489  11735  Z= 0.380
  Chirality :  0.049   0.159   1395
  Planarity :  0.006   0.051   1440
  Dihedral  :  5.739  32.412   1202
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 10.85 %
    Favored  : 85.68 %
  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: -2.98 (0.24), residues: 1070
  helix: -1.39 (0.19), residues: 606
  sheet: -2.65 (0.46), residues: 94
  loop : -2.56 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP C 426 
 HIS   0.008   0.002   HIS C 427 
 PHE   0.032   0.002   PHE A 203 
 TYR   0.017   0.002   TYR C 526 
 ARG   0.008   0.001   ARG A 158 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 0.905 
Fit side-chains
REVERT: C  468 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8087 (ttp-170)
  outliers start: 32
  outliers final: 22
  residues processed: 121
  average time/residue: 1.2809
  time to fit residues: 164.8821
Evaluate side-chains
  122 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  403 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  382 CYS
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  468 ARG
Chi-restraints excluded: chain C residue  545 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0270
   chunk 25 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 86 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    7.9990
   overall best weight:    0.6440

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   8655  Z= 0.153
  Angle     :  0.560   6.197  11735  Z= 0.287
  Chirality :  0.040   0.147   1395
  Planarity :  0.004   0.040   1440
  Dihedral  :  4.961  33.285   1202
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 11.82 %
    Favored  : 85.57 %
  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: -2.24 (0.25), residues: 1070
  helix: -0.77 (0.21), residues: 602
  sheet: -2.33 (0.45), residues: 102
  loop : -2.26 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 426 
 HIS   0.004   0.001   HIS A 219 
 PHE   0.017   0.001   PHE A 203 
 TYR   0.010   0.001   TYR C 526 
 ARG   0.008   0.000   ARG A 205 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.929 
Fit side-chains
REVERT: A  211 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7470 (mt-10)
REVERT: A  274 MET cc_start: 0.7841 (mtt) cc_final: 0.7564 (mtt)
REVERT: C  211 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7463 (mt-10)
REVERT: C  468 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7804 (ttp-170)
  outliers start: 24
  outliers final: 18
  residues processed: 124
  average time/residue: 1.1372
  time to fit residues: 151.5341
Evaluate side-chains
  121 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  403 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  382 CYS
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  468 ARG
Chi-restraints excluded: chain C residue  476 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 104 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
C 130 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8655  Z= 0.244
  Angle     :  0.609   6.991  11735  Z= 0.307
  Chirality :  0.042   0.151   1395
  Planarity :  0.004   0.041   1440
  Dihedral  :  5.072  33.521   1202
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 12.15 %
    Favored  : 84.49 %
  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: -2.03 (0.25), residues: 1070
  helix: -0.66 (0.21), residues: 602
  sheet: -1.91 (0.48), residues: 96
  loop : -2.15 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 426 
 HIS   0.005   0.001   HIS A 219 
 PHE   0.019   0.002   PHE C 502 
 TYR   0.012   0.001   TYR C 526 
 ARG   0.008   0.001   ARG C 158 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A  211 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7485 (mt-10)
REVERT: C   97 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8213 (ttt)
REVERT: C  211 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7473 (mt-10)
REVERT: C  468 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8165 (ttp-170)
  outliers start: 31
  outliers final: 24
  residues processed: 126
  average time/residue: 1.1143
  time to fit residues: 150.5787
Evaluate side-chains
  131 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  403 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  382 CYS
Chi-restraints excluded: chain C residue  398 LEU
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  468 ARG
Chi-restraints excluded: chain C residue  476 THR
Chi-restraints excluded: chain C residue  635 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0010
   chunk 51 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
C 130 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   8655  Z= 0.152
  Angle     :  0.535   5.824  11735  Z= 0.272
  Chirality :  0.040   0.145   1395
  Planarity :  0.004   0.039   1440
  Dihedral  :  4.725  33.464   1202
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 12.47 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.26), residues: 1070
  helix: -0.34 (0.21), residues: 602
  sheet: -2.02 (0.48), residues: 102
  loop : -2.01 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 426 
 HIS   0.004   0.001   HIS C 219 
 PHE   0.020   0.001   PHE A 502 
 TYR   0.009   0.001   TYR C 586 
 ARG   0.008   0.000   ARG C 158 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.932 
Fit side-chains
REVERT: A  211 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7457 (mt-10)
REVERT: C   97 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8161 (ttt)
REVERT: C  188 GLU cc_start: 0.6796 (tt0) cc_final: 0.6589 (tm-30)
REVERT: C  211 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7434 (mt-10)
REVERT: C  468 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7829 (ttp-170)
  outliers start: 27
  outliers final: 22
  residues processed: 134
  average time/residue: 1.0868
  time to fit residues: 156.5660
Evaluate side-chains
  135 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  382 CYS
Chi-restraints excluded: chain A residue  403 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  382 CYS
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  468 ARG
Chi-restraints excluded: chain C residue  476 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 99 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 29 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
C 130 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8655  Z= 0.171
  Angle     :  0.547   6.013  11735  Z= 0.277
  Chirality :  0.040   0.149   1395
  Planarity :  0.004   0.042   1440
  Dihedral  :  4.707  33.652   1202
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.10 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.26), residues: 1070
  helix: -0.24 (0.21), residues: 604
  sheet: -1.94 (0.52), residues: 92
  loop : -1.92 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 426 
 HIS   0.004   0.001   HIS A 219 
 PHE   0.022   0.001   PHE A 502 
 TYR   0.011   0.001   TYR A 586 
 ARG   0.009   0.000   ARG C 158 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 1.025 
Fit side-chains
REVERT: A  211 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7445 (mt-10)
REVERT: A  232 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7974 (mt-10)
REVERT: C   97 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8169 (ttt)
REVERT: C  211 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7423 (mt-10)
REVERT: C  468 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7847 (ttp-170)
  outliers start: 23
  outliers final: 21
  residues processed: 129
  average time/residue: 1.1018
  time to fit residues: 152.5126
Evaluate side-chains
  137 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  382 CYS
Chi-restraints excluded: chain A residue  403 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  382 CYS
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  468 ARG
Chi-restraints excluded: chain C residue  476 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    0.3980
   chunk 62 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0970
   chunk 107 optimal weight:    0.9980
   chunk 99 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
A 147 GLN
C 130 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   8655  Z= 0.143
  Angle     :  0.523   5.544  11735  Z= 0.266
  Chirality :  0.039   0.144   1395
  Planarity :  0.004   0.040   1440
  Dihedral  :  4.554  33.682   1202
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.21 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.26), residues: 1070
  helix: -0.01 (0.21), residues: 600
  sheet: -1.74 (0.50), residues: 102
  loop : -1.82 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 426 
 HIS   0.003   0.001   HIS A 219 
 PHE   0.024   0.001   PHE C 502 
 TYR   0.009   0.001   TYR A 586 
 ARG   0.009   0.000   ARG A 158 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A  211 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7423 (mt-10)
REVERT: C   97 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8156 (ttt)
REVERT: C  147 GLN cc_start: 0.7680 (tt0) cc_final: 0.7469 (tt0)
REVERT: C  211 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7397 (mt-10)
REVERT: C  468 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7808 (ttp-170)
  outliers start: 23
  outliers final: 19
  residues processed: 134
  average time/residue: 0.9933
  time to fit residues: 143.8574
Evaluate side-chains
  132 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  382 CYS
Chi-restraints excluded: chain A residue  403 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  382 CYS
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  468 ARG
Chi-restraints excluded: chain C residue  476 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
C 130 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.166854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.124647 restraints weight = 8945.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.73
r_work: 0.3152 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8655  Z= 0.181
  Angle     :  0.558   6.736  11735  Z= 0.282
  Chirality :  0.040   0.149   1395
  Planarity :  0.004   0.043   1440
  Dihedral  :  4.629  33.753   1202
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.08 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.26), residues: 1070
  helix: -0.03 (0.21), residues: 602
  sheet: -1.78 (0.53), residues: 92
  loop : -1.78 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 426 
 HIS   0.004   0.001   HIS A 219 
 PHE   0.025   0.001   PHE A 502 
 TYR   0.011   0.001   TYR A 586 
 ARG   0.009   0.000   ARG C 158 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3115.63 seconds
wall clock time: 56 minutes 52.84 seconds (3412.84 seconds total)