Starting phenix.real_space_refine
on Sat Jan 18 19:06:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ce0_45489/01_2025/9ce0_45489_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ce0_45489/01_2025/9ce0_45489.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ce0_45489/01_2025/9ce0_45489.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ce0_45489/01_2025/9ce0_45489.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ce0_45489/01_2025/9ce0_45489_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ce0_45489/01_2025/9ce0_45489_neut.cif"
  }
  resolution = 3.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     S      66      5.16       5
     C    7957      2.51       5
     N    2188      2.21       5
     O    2338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 120 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12551
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 6257
          Classifications: {'peptide': 787}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 33, 'TRANS': 750}
    Chain: "B"
      Number of atoms: 6204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 781, 6204
          Classifications: {'peptide': 781}
          Link IDs: {'PTRANS': 35, 'TRANS': 745}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.19, per 1000 atoms: 0.57
  Number of scatterers: 12551
  At special positions: 0
  Unit cell: (93.6383, 103.325, 195.349, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      2     26.01
     S      66     16.00
     O    2338      8.00
     N    2188      7.00
     C    7957      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.32
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2956

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 13 sheets defined
      51.0% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 28
      removed outlier: 3.802A  pdb=" N   ALA A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 56 through 61
      removed outlier: 3.810A  pdb=" N   VAL A  60 " --> pdb=" O   LYS A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 68
      removed outlier: 3.929A  pdb=" N   MET A  67 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 87
      removed outlier: 3.647A  pdb=" N   TYR A  80 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY A  87 " --> pdb=" O   HIS A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 92
    Processing helix  chain 'A' and resid 119 through 123
    Processing helix  chain 'A' and resid 133 through 152
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 180 through 185
    Processing helix  chain 'A' and resid 188 through 193
    Processing helix  chain 'A' and resid 200 through 212
      removed outlier: 4.202A  pdb=" N   ILE A 204 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 275
    Processing helix  chain 'A' and resid 278 through 294
    Processing helix  chain 'A' and resid 352 through 383
    Processing helix  chain 'A' and resid 394 through 409
    Processing helix  chain 'A' and resid 421 through 429
    Processing helix  chain 'A' and resid 430 through 449
      removed outlier: 4.219A  pdb=" N   GLN A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLU A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 485
    Processing helix  chain 'A' and resid 512 through 531
    Processing helix  chain 'A' and resid 542 through 563
      removed outlier: 3.627A  pdb=" N   ARG A 549 " --> pdb=" O   MET A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 609
      Proline residue:  A 604  - end of helix
    Processing helix  chain 'A' and resid 611 through 634
    Processing helix  chain 'A' and resid 645 through 648
    Processing helix  chain 'A' and resid 650 through 652
      No H-bonds generated for 'chain 'A' and resid 650 through 652'
    Processing helix  chain 'A' and resid 653 through 665
      removed outlier: 4.265A  pdb=" N   ALA A 661 " --> pdb=" O   GLN A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 699
    Processing helix  chain 'A' and resid 710 through 720
      removed outlier: 3.758A  pdb=" N   LEU A 720 " --> pdb=" O   ARG A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 736
      removed outlier: 3.813A  pdb=" N   ARG A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   LEU A 736 " --> pdb=" O   VAL A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 756
      removed outlier: 3.615A  pdb=" N   LEU A 742 " --> pdb=" O   GLU A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 777
    Processing helix  chain 'A' and resid 794 through 803
      removed outlier: 3.859A  pdb=" N   SER A 800 " --> pdb=" O   PRO A 796 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 28
    Processing helix  chain 'B' and resid 46 through 54
    Processing helix  chain 'B' and resid 56 through 61
    Processing helix  chain 'B' and resid 64 through 68
    Processing helix  chain 'B' and resid 73 through 75
      No H-bonds generated for 'chain 'B' and resid 73 through 75'
    Processing helix  chain 'B' and resid 76 through 88
      removed outlier: 3.621A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 92
    Processing helix  chain 'B' and resid 134 through 153
    Processing helix  chain 'B' and resid 170 through 178
    Processing helix  chain 'B' and resid 180 through 185
    Processing helix  chain 'B' and resid 188 through 193
    Processing helix  chain 'B' and resid 201 through 210
      removed outlier: 4.054A  pdb=" N   ARG B 205 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 276
    Processing helix  chain 'B' and resid 278 through 294
    Processing helix  chain 'B' and resid 352 through 377
    Processing helix  chain 'B' and resid 394 through 408
      removed outlier: 3.686A  pdb=" N   LYS B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 447
      removed outlier: 4.142A  pdb=" N   VAL B 425 " --> pdb=" O   HIS B 421 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   TYR B 431 " --> pdb=" O   ASP B 427 " (cutoff:3.500A)
      removed outlier: 9.336A  pdb=" N   ALA B 432 " --> pdb=" O   SER B 428 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   TRP B 433 " --> pdb=" O   LEU B 429 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU B 447 " --> pdb=" O   ASN B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 486
      removed outlier: 3.755A  pdb=" N   VAL B 486 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 531
    Processing helix  chain 'B' and resid 539 through 562
    Processing helix  chain 'B' and resid 598 through 610
      Proline residue:  B 604  - end of helix
    Processing helix  chain 'B' and resid 611 through 632
    Processing helix  chain 'B' and resid 643 through 648
    Processing helix  chain 'B' and resid 650 through 654
      removed outlier: 3.921A  pdb=" N   GLN B 653 " --> pdb=" O   ARG B 650 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LEU B 654 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 650 through 654'
    Processing helix  chain 'B' and resid 655 through 665
      removed outlier: 4.914A  pdb=" N   ALA B 661 " --> pdb=" O   GLN B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 683
    Processing helix  chain 'B' and resid 686 through 699
      removed outlier: 3.706A  pdb=" N   LYS B 690 " --> pdb=" O   THR B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 720
    Processing helix  chain 'B' and resid 728 through 733
    Processing helix  chain 'B' and resid 738 through 755
    Processing helix  chain 'B' and resid 766 through 776
    Processing helix  chain 'B' and resid 794 through 802
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36
    Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168
      removed outlier: 3.764A  pdb=" N   GLN A 168 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 314
      removed outlier: 6.615A  pdb=" N   LEU A 301 " --> pdb=" O   TRP A 312 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER A 314 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   VAL A 299 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLN A 343 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ALA A 339 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE A 331 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ALA A 329 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   GLN A 343 " --> pdb=" O   TRP A 327 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TRP A 327 " --> pdb=" O   GLN A 343 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   LYS A 345 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   GLN A 325 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 459
      removed outlier: 5.507A  pdb=" N   LEU A 455 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   VAL A 466 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   ARG A 457 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   VAL A 464 " --> pdb=" O   ARG A 457 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU A 459 " --> pdb=" O   GLN A 462 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 490 through 492
    Processing sheet with id=AA6, first strand: chain 'A' and resid 566 through 573
      removed outlier: 4.453A  pdb=" N   TRP A 589 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 566 through 573
      removed outlier: 4.652A  pdb=" N   ASN A 643 " --> pdb=" O   ALA A 585 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   ALA A 587 " --> pdb=" O   ASN A 643 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU A 675 " --> pdb=" O   VAL A 642 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLY A 701 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LEU A 702 " --> pdb=" O   GLU A 724 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   LYS A 726 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL A 704 " --> pdb=" O   LYS A 726 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ILE A 725 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A 725 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ILE A 727 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   VAL A 764 " --> pdb=" O   ILE A 727 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   GLN A 782 " --> pdb=" O   VAL A 759 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   ALA A 761 " --> pdb=" O   GLN A 782 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45
      removed outlier: 6.673A  pdb=" N   LEU B  35 " --> pdb=" O   MET B  43 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   PHE B  45 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   ALA B  33 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   GLY B  32 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 168
      removed outlier: 6.055A  pdb=" N   VAL B 159 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 308 through 314
      removed outlier: 6.714A  pdb=" N   LEU B 301 " --> pdb=" O   TRP B 312 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   SER B 314 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   VAL B 299 " --> pdb=" O   SER B 314 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA B 339 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   ILE B 331 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ILE B 341 " --> pdb=" O   ALA B 329 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ALA B 329 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   GLN B 343 " --> pdb=" O   TRP B 327 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   TRP B 327 " --> pdb=" O   GLN B 343 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   LYS B 345 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   GLN B 325 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 454 through 459
      removed outlier: 7.109A  pdb=" N   GLN B 462 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 672 through 674
      removed outlier: 6.344A  pdb=" N   LEU B 640 " --> pdb=" O   THR B 673 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   SER B 641 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ILE B 583 " --> pdb=" O   SER B 641 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   GLN B 572 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE B 583 " --> pdb=" O   GLN B 570 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   GLN B 570 " --> pdb=" O   ILE B 583 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ALA B 585 " --> pdb=" O   VAL B 568 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL B 568 " --> pdb=" O   ALA B 585 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   ALA B 587 " --> pdb=" O   LYS B 566 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   LYS B 566 " --> pdb=" O   ALA B 587 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   VAL B 759 " --> pdb=" O   VAL B 780 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ILE B 725 " --> pdb=" O   VAL B 760 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 590 through 591

    696 hydrogen bonds defined for protein.
    1998 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: 5.12

  Time building geometry restraints manager: 3.74 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 4943
        1.38 -     1.56: 7750
        1.56 -     1.73: 0
        1.73 -     1.91: 116
        1.91 -     2.08: 8
  Bond restraints: 12817
  Sorted by residual:
  bond pdb=" CA  SER A 600 "
       pdb=" C   SER A 600 "
    ideal  model  delta    sigma   weight residual
    1.522  1.475  0.047 1.45e-02 4.76e+03 1.03e+01
  bond pdb=" N   PHE B 386 "
       pdb=" CA  PHE B 386 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.13e-02 7.83e+03 6.19e+00
  bond pdb=" N   ILE B 384 "
       pdb=" CA  ILE B 384 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.90e-02 2.77e+03 3.60e+00
  bond pdb=" N   GLN B 385 "
       pdb=" CA  GLN B 385 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.58e-02 4.01e+03 3.56e+00
  bond pdb=" C   ASP B 387 "
       pdb=" N   PRO B 388 "
    ideal  model  delta    sigma   weight residual
    1.334  1.347 -0.013 8.40e-03 1.42e+04 2.37e+00
  ... (remaining 12812 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 16472
        1.45 -     2.90: 803
        2.90 -     4.36: 102
        4.36 -     5.81: 8
        5.81 -     7.26: 3
  Bond angle restraints: 17388
  Sorted by residual:
  angle pdb=" N   ILE A 148 "
        pdb=" CA  ILE A 148 "
        pdb=" C   ILE A 148 "
      ideal   model   delta    sigma   weight residual
     110.72  106.18    4.54 1.01e+00 9.80e-01 2.02e+01
  angle pdb=" N   ARG A 779 "
        pdb=" CA  ARG A 779 "
        pdb=" CB  ARG A 779 "
      ideal   model   delta    sigma   weight residual
     114.17  109.61    4.56 1.14e+00 7.69e-01 1.60e+01
  angle pdb=" C   GLU B 793 "
        pdb=" N   GLU B 794 "
        pdb=" CA  GLU B 794 "
      ideal   model   delta    sigma   weight residual
     121.54  128.65   -7.11 1.91e+00 2.74e-01 1.39e+01
  angle pdb=" N   GLN B 385 "
        pdb=" CA  GLN B 385 "
        pdb=" C   GLN B 385 "
      ideal   model   delta    sigma   weight residual
     113.40  108.14    5.26 1.47e+00 4.63e-01 1.28e+01
  angle pdb=" N   ASP A 151 "
        pdb=" CA  ASP A 151 "
        pdb=" C   ASP A 151 "
      ideal   model   delta    sigma   weight residual
     111.28  107.61    3.67 1.09e+00 8.42e-01 1.13e+01
  ... (remaining 17383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 6911
       17.75 -    35.50: 648
       35.50 -    53.25: 127
       53.25 -    71.00: 41
       71.00 -    88.75: 17
  Dihedral angle restraints: 7744
    sinusoidal: 3191
      harmonic: 4553
  Sorted by residual:
  dihedral pdb=" CA  GLN B 657 "
           pdb=" C   GLN B 657 "
           pdb=" N   VAL B 658 "
           pdb=" CA  VAL B 658 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.15   28.85     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  GLY A 227 "
           pdb=" C   GLY A 227 "
           pdb=" N   GLU A 228 "
           pdb=" CA  GLU A 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.83  -28.17     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  LEU A 720 "
           pdb=" C   LEU A 720 "
           pdb=" N   PRO A 721 "
           pdb=" CA  PRO A 721 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.42  -25.58     0      5.00e+00 4.00e-02 2.62e+01
  ... (remaining 7741 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1405
       0.040 -    0.080: 363
       0.080 -    0.120: 137
       0.120 -    0.160: 16
       0.160 -    0.200: 1
  Chirality restraints: 1922
  Sorted by residual:
  chirality pdb=" CA  ILE B 384 "
            pdb=" N   ILE B 384 "
            pdb=" C   ILE B 384 "
            pdb=" CB  ILE B 384 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  ILE A 331 "
            pdb=" N   ILE A 331 "
            pdb=" C   ILE A 331 "
            pdb=" CB  ILE A 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  ILE A  69 "
            pdb=" N   ILE A  69 "
            pdb=" C   ILE A  69 "
            pdb=" CB  ILE A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 1919 not shown)

  Planarity restraints: 2261
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 155 "   -0.037 5.00e-02 4.00e+02   5.58e-02 4.98e+00
        pdb=" N   PRO A 156 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 156 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 156 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 266 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.93e+00
        pdb=" C   GLU B 266 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   GLU B 266 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY B 267 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 144 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.57e+00
        pdb=" C   ARG B 144 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ARG B 144 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLN B 145 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2258 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 184
        2.52 -     3.12: 10812
        3.12 -     3.71: 20858
        3.71 -     4.31: 27856
        4.31 -     4.90: 45103
  Nonbonded interactions: 104813
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 140 "
            pdb=" OG1 THR A 143 "
     model   vdw
     1.931 3.040
  nonbonded pdb=" O   ALA A 272 "
            pdb=" OG  SER A 275 "
     model   vdw
     1.963 3.040
  nonbonded pdb=" O   ASN A  84 "
            pdb=" OH  TYR A 126 "
     model   vdw
     1.979 3.040
  nonbonded pdb=" OG  SER B 632 "
            pdb=" OE1 GLN B 633 "
     model   vdw
     1.997 3.040
  nonbonded pdb=" O   GLY B 708 "
            pdb=" OG1 THR B 709 "
     model   vdw
     2.048 3.040
  ... (remaining 104808 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' and (resid 20 through 377 or resid 384 through 806 or resid 901 throu \ 
gh 902))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     30.480
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
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      :  0.004   0.047  12817  Z= 0.271
  Angle     :  0.693   7.261  17388  Z= 0.460
  Chirality :  0.042   0.200   1922
  Planarity :  0.006   0.069   2261
  Dihedral  : 15.095  88.749   4788
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.27 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  9.12 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    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: -1.00 (0.21), residues: 1562
  helix:  0.30 (0.20), residues: 713
  sheet: -0.96 (0.29), residues: 322
  loop : -1.66 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 665 
 HIS   0.005   0.001   HIS A 365 
 PHE   0.022   0.002   PHE A 602 
 TYR   0.018   0.001   TYR B 454 
 ARG   0.004   0.001   ARG B 164 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 138
  time to evaluate  : 1.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 MET cc_start: -0.0135 (ptm) cc_final: -0.0391 (ptt)
REVERT: A   43 MET cc_start: 0.2565 (mpp) cc_final: 0.2218 (mpp)
REVERT: B  416 LEU cc_start: 0.9074 (tp) cc_final: 0.8351 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2902
  time to fit residues: 57.0783
Evaluate side-chains
  88 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0870
   chunk 40 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 63 optimal weight:    0.3980
   chunk 122 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 141 optimal weight:    4.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
A 343 GLN
** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 HIS
B 139 GLN
B 142 GLN
B 217 GLN
B 248 ASN
** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.070064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.046589 restraints weight = 93483.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.046137 restraints weight = 72814.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.046733 restraints weight = 57337.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12817  Z= 0.234
  Angle     :  0.748   8.918  17388  Z= 0.379
  Chirality :  0.047   0.198   1922
  Planarity :  0.006   0.062   2261
  Dihedral  :  6.400  76.350   1707
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.67 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.16 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.22), residues: 1562
  helix:  0.36 (0.19), residues: 719
  sheet: -0.76 (0.28), residues: 340
  loop : -1.34 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 589 
 HIS   0.007   0.001   HIS A  77 
 PHE   0.024   0.002   PHE B 602 
 TYR   0.016   0.002   TYR B 179 
 ARG   0.005   0.001   ARG B 225 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 1.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 PHE cc_start: -0.2666 (t80) cc_final: -0.3221 (t80)
REVERT: A  343 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.9119 (tm-30)
REVERT: A  682 MET cc_start: 0.8985 (mmm) cc_final: 0.8652 (mmm)
REVERT: B  253 PHE cc_start: 0.8698 (m-80) cc_final: 0.8292 (m-10)
REVERT: B  282 MET cc_start: 0.8236 (mtt) cc_final: 0.8013 (mpp)
REVERT: B  772 MET cc_start: 0.9309 (mtm) cc_final: 0.9010 (ptp)
  outliers start: 21
  outliers final: 5
  residues processed: 106
  average time/residue: 0.2514
  time to fit residues: 39.4301
Evaluate side-chains
  83 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain B residue  142 GLN
Chi-restraints excluded: chain B residue  205 ARG
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 110 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 152 optimal weight:    3.9990
   chunk 1 optimal weight:   20.0000
   chunk 9 optimal weight:    7.9990
   chunk 57 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 141 optimal weight:    4.9990
   chunk 122 optimal weight:    0.6980
   chunk 128 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 HIS
A 663 HIS
B 152 HIS
B 248 ASN
B 397 ASN
** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.066489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.043262 restraints weight = 97491.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.042678 restraints weight = 78504.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.043213 restraints weight = 63420.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.093  12817  Z= 0.393
  Angle     :  0.779   8.428  17388  Z= 0.401
  Chirality :  0.047   0.185   1922
  Planarity :  0.006   0.057   2261
  Dihedral  :  6.413  71.294   1707
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.38 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.68 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.21), residues: 1562
  helix:  0.20 (0.19), residues: 709
  sheet: -0.77 (0.28), residues: 340
  loop : -1.26 (0.29), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 665 
 HIS   0.008   0.002   HIS A 521 
 PHE   0.025   0.003   PHE A 602 
 TYR   0.022   0.002   TYR B 454 
 ARG   0.009   0.001   ARG A 112 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 76
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 MET cc_start: 0.8142 (ttt) cc_final: 0.7893 (ptm)
REVERT: A  389 MET cc_start: 0.8685 (tmm) cc_final: 0.8248 (tmm)
REVERT: A  682 MET cc_start: 0.9376 (mmm) cc_final: 0.9014 (mmm)
REVERT: A  698 MET cc_start: 0.9394 (mpp) cc_final: 0.9098 (mpp)
REVERT: A  772 MET cc_start: 0.8626 (mtp) cc_final: 0.8385 (mtp)
REVERT: B  282 MET cc_start: 0.8326 (mtt) cc_final: 0.8053 (ptp)
REVERT: B  772 MET cc_start: 0.9549 (mtm) cc_final: 0.9154 (ptp)
REVERT: B  799 MET cc_start: 0.9250 (ttt) cc_final: 0.8279 (ppp)
  outliers start: 39
  outliers final: 14
  residues processed: 108
  average time/residue: 0.2613
  time to fit residues: 41.6291
Evaluate side-chains
  88 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 1.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain B residue  142 GLN
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 110 optimal weight:    9.9990
   chunk 1 optimal weight:   30.0000
   chunk 0 optimal weight:   30.0000
   chunk 127 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    0.2980
   chunk 38 optimal weight:    0.8980
   chunk 79 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 108 optimal weight:    8.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 GLN
** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.067058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.043658 restraints weight = 96971.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.042866 restraints weight = 76970.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.043347 restraints weight = 62344.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12817  Z= 0.252
  Angle     :  0.705  10.065  17388  Z= 0.355
  Chirality :  0.044   0.155   1922
  Planarity :  0.005   0.046   2261
  Dihedral  :  6.262  68.841   1707
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.25 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.90 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.22), residues: 1562
  helix:  0.44 (0.19), residues: 703
  sheet: -0.70 (0.28), residues: 341
  loop : -1.23 (0.29), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 665 
 HIS   0.007   0.001   HIS B 152 
 PHE   0.024   0.002   PHE A 602 
 TYR   0.013   0.001   TYR B 454 
 ARG   0.020   0.001   ARG B 171 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 75
  time to evaluate  : 1.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9787 (tpp) cc_final: 0.9223 (mmm)
REVERT: A  389 MET cc_start: 0.8701 (tmm) cc_final: 0.8251 (tmm)
REVERT: A  682 MET cc_start: 0.9386 (mmm) cc_final: 0.9169 (mmm)
REVERT: A  698 MET cc_start: 0.9477 (mpp) cc_final: 0.9154 (mpp)
REVERT: A  717 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9299 (mt)
REVERT: A  758 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8708 (p)
REVERT: A  772 MET cc_start: 0.8574 (mtp) cc_final: 0.8338 (mtp)
REVERT: B  139 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8823 (tm-30)
REVERT: B  253 PHE cc_start: 0.8508 (m-10) cc_final: 0.7996 (m-80)
REVERT: B  542 MET cc_start: 0.9192 (ptt) cc_final: 0.8799 (ptt)
REVERT: B  545 MET cc_start: 0.9206 (tmm) cc_final: 0.8869 (tmm)
REVERT: B  772 MET cc_start: 0.9585 (mtm) cc_final: 0.9155 (ptp)
  outliers start: 37
  outliers final: 18
  residues processed: 105
  average time/residue: 0.2412
  time to fit residues: 39.5745
Evaluate side-chains
  93 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 1.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 121 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 52 optimal weight:    0.8980
   chunk 138 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0670
   chunk 126 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 91 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0040
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.5130

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

Flipped N/Q/H residues before XYZ refinement:
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 GLN
B 653 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.068126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.044988 restraints weight = 95050.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.044484 restraints weight = 74598.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.044915 restraints weight = 58675.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12817  Z= 0.185
  Angle     :  0.687   9.979  17388  Z= 0.341
  Chirality :  0.044   0.195   1922
  Planarity :  0.005   0.056   2261
  Dihedral  :  6.116  69.418   1707
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.51 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.41 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.22), residues: 1562
  helix:  0.57 (0.20), residues: 711
  sheet: -0.58 (0.28), residues: 324
  loop : -1.02 (0.29), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 110 
 HIS   0.004   0.001   HIS A  77 
 PHE   0.023   0.002   PHE A 602 
 TYR   0.007   0.001   TYR B 454 
 ARG   0.005   0.000   ARG B 171 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 77
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASN cc_start: 0.9540 (m110) cc_final: 0.9170 (p0)
REVERT: A  389 MET cc_start: 0.8644 (tmm) cc_final: 0.8185 (tmm)
REVERT: A  681 MET cc_start: 0.9371 (tpp) cc_final: 0.9122 (tpp)
REVERT: A  717 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9278 (mt)
REVERT: A  772 MET cc_start: 0.8469 (mtp) cc_final: 0.8243 (mtp)
REVERT: B   30 MET cc_start: -0.2921 (tpt) cc_final: -0.3254 (tpt)
REVERT: B   43 MET cc_start: 0.0593 (mtp) cc_final: 0.0362 (mpp)
REVERT: B  131 ARG cc_start: 0.9030 (mmp80) cc_final: 0.8795 (tmt170)
REVERT: B  282 MET cc_start: 0.8494 (ptp) cc_final: 0.8290 (mpp)
REVERT: B  542 MET cc_start: 0.9144 (ptt) cc_final: 0.8761 (ptt)
REVERT: B  545 MET cc_start: 0.9122 (tmm) cc_final: 0.8803 (tmm)
REVERT: B  772 MET cc_start: 0.9593 (mtm) cc_final: 0.9130 (ptp)
REVERT: B  787 SER cc_start: 0.9178 (OUTLIER) cc_final: 0.8850 (p)
REVERT: B  795 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8751 (mm)
  outliers start: 35
  outliers final: 19
  residues processed: 105
  average time/residue: 0.2410
  time to fit residues: 38.9249
Evaluate side-chains
  96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  787 SER
Chi-restraints excluded: chain B residue  795 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 80 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 6 optimal weight:   20.0000
   chunk 146 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   overall best weight:    1.8988

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

Flipped N/Q/H residues before XYZ refinement:
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.066480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.043396 restraints weight = 100195.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.042692 restraints weight = 78954.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.042991 restraints weight = 64081.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  12817  Z= 0.277
  Angle     :  0.719   9.429  17388  Z= 0.357
  Chirality :  0.045   0.290   1922
  Planarity :  0.005   0.052   2261
  Dihedral  :  6.075  68.002   1707
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.44 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.37 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.22), residues: 1562
  helix:  0.62 (0.19), residues: 718
  sheet: -0.61 (0.28), residues: 329
  loop : -1.16 (0.29), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 665 
 HIS   0.005   0.001   HIS A 521 
 PHE   0.024   0.002   PHE A 602 
 TYR   0.014   0.001   TYR B 454 
 ARG   0.005   0.000   ARG B 395 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 74
  time to evaluate  : 1.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8661 (mmt)
REVERT: A  308 MET cc_start: 0.9811 (tpp) cc_final: 0.9604 (tpt)
REVERT: A  389 MET cc_start: 0.8785 (tmm) cc_final: 0.8258 (tmm)
REVERT: A  456 CYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7277 (t)
REVERT: A  698 MET cc_start: 0.9435 (mpp) cc_final: 0.9180 (mpp)
REVERT: A  717 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9316 (mt)
REVERT: A  772 MET cc_start: 0.8481 (mtp) cc_final: 0.8261 (mtp)
REVERT: B   43 MET cc_start: 0.0602 (mtp) cc_final: 0.0375 (mpp)
REVERT: B  419 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8474 (p)
REVERT: B  542 MET cc_start: 0.9175 (ptt) cc_final: 0.8792 (ptt)
REVERT: B  545 MET cc_start: 0.9166 (tmm) cc_final: 0.8857 (tmm)
REVERT: B  772 MET cc_start: 0.9583 (mtm) cc_final: 0.9105 (ptp)
REVERT: B  795 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8933 (mm)
REVERT: B  799 MET cc_start: 0.9087 (ttt) cc_final: 0.8246 (ppp)
  outliers start: 33
  outliers final: 20
  residues processed: 101
  average time/residue: 0.2356
  time to fit residues: 38.0530
Evaluate side-chains
  95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  580 LEU
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  795 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 105 optimal weight:    0.5980
   chunk 90 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 122 optimal weight:    6.9990
   chunk 145 optimal weight:    0.6980
   chunk 137 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.067379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.044363 restraints weight = 97662.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.043693 restraints weight = 76711.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.044116 restraints weight = 61444.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12817  Z= 0.203
  Angle     :  0.702  11.535  17388  Z= 0.345
  Chirality :  0.044   0.213   1922
  Planarity :  0.005   0.054   2261
  Dihedral  :  6.005  68.468   1707
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.96 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.22), residues: 1562
  helix:  0.73 (0.20), residues: 712
  sheet: -0.52 (0.28), residues: 323
  loop : -1.03 (0.29), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 231 
 HIS   0.004   0.001   HIS A  77 
 PHE   0.025   0.002   PHE B 177 
 TYR   0.008   0.001   TYR B 454 
 ARG   0.003   0.000   ARG B 288 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASN cc_start: 0.9407 (m110) cc_final: 0.9132 (p0)
REVERT: A  389 MET cc_start: 0.8781 (tmm) cc_final: 0.8237 (tmm)
REVERT: A  456 CYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7046 (t)
REVERT: A  552 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9481 (tp)
REVERT: A  680 MET cc_start: 0.8647 (ptt) cc_final: 0.8264 (pmm)
REVERT: A  698 MET cc_start: 0.9465 (mpp) cc_final: 0.9198 (mpp)
REVERT: A  717 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9367 (mt)
REVERT: A  772 MET cc_start: 0.8461 (mtp) cc_final: 0.8248 (mtp)
REVERT: B   30 MET cc_start: -0.2711 (tpt) cc_final: -0.3168 (tpt)
REVERT: B   43 MET cc_start: 0.0649 (mtp) cc_final: 0.0421 (mpp)
REVERT: B  419 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8417 (p)
REVERT: B  542 MET cc_start: 0.9192 (ptt) cc_final: 0.8805 (ptt)
REVERT: B  545 MET cc_start: 0.9166 (tmm) cc_final: 0.8816 (tmm)
REVERT: B  772 MET cc_start: 0.9624 (mtm) cc_final: 0.9142 (ptp)
REVERT: B  799 MET cc_start: 0.9061 (ttt) cc_final: 0.8038 (ppp)
  outliers start: 27
  outliers final: 19
  residues processed: 94
  average time/residue: 0.2340
  time to fit residues: 34.3875
Evaluate side-chains
  92 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0060
   chunk 6 optimal weight:   20.0000
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:   10.0000
   chunk 99 optimal weight:    7.9990
   chunk 106 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0270
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.067953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.044680 restraints weight = 96886.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.043950 restraints weight = 76274.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.044432 restraints weight = 62192.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12817  Z= 0.182
  Angle     :  0.716  14.156  17388  Z= 0.348
  Chirality :  0.044   0.176   1922
  Planarity :  0.005   0.054   2261
  Dihedral  :  5.961  69.768   1707
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.69 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.22), residues: 1562
  helix:  0.74 (0.20), residues: 713
  sheet: -0.48 (0.28), residues: 323
  loop : -1.01 (0.29), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 231 
 HIS   0.004   0.001   HIS A  77 
 PHE   0.021   0.001   PHE A 602 
 TYR   0.007   0.001   TYR A 526 
 ARG   0.003   0.000   ARG B 631 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 1.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 MET cc_start: 0.8011 (mmt) cc_final: 0.7605 (mmm)
REVERT: A  323 ASN cc_start: 0.9440 (m110) cc_final: 0.9150 (p0)
REVERT: A  389 MET cc_start: 0.8715 (tmm) cc_final: 0.8204 (tmm)
REVERT: A  456 CYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6878 (t)
REVERT: A  680 MET cc_start: 0.8520 (ptt) cc_final: 0.8211 (pmm)
REVERT: A  698 MET cc_start: 0.9418 (mpp) cc_final: 0.9157 (mpp)
REVERT: A  717 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9341 (mt)
REVERT: A  772 MET cc_start: 0.8417 (mtp) cc_final: 0.8212 (mtp)
REVERT: B  542 MET cc_start: 0.9173 (ptt) cc_final: 0.8793 (ptt)
REVERT: B  545 MET cc_start: 0.9151 (tmm) cc_final: 0.8809 (tmm)
REVERT: B  772 MET cc_start: 0.9626 (mtm) cc_final: 0.9149 (ptp)
REVERT: B  799 MET cc_start: 0.8903 (ttt) cc_final: 0.7956 (ppp)
  outliers start: 24
  outliers final: 17
  residues processed: 90
  average time/residue: 0.2038
  time to fit residues: 30.1511
Evaluate side-chains
  88 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 1.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 39 optimal weight:    0.1980
   chunk 105 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 154 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 134 optimal weight:    0.0670
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.067772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.044924 restraints weight = 98671.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.044367 restraints weight = 76631.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.044687 restraints weight = 61573.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.4173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12817  Z= 0.193
  Angle     :  0.716  10.006  17388  Z= 0.349
  Chirality :  0.044   0.213   1922
  Planarity :  0.005   0.048   2261
  Dihedral  :  5.906  70.840   1707
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.47 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.22), residues: 1562
  helix:  0.79 (0.20), residues: 718
  sheet: -0.44 (0.29), residues: 317
  loop : -1.01 (0.29), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 110 
 HIS   0.003   0.001   HIS A  77 
 PHE   0.021   0.002   PHE B 602 
 TYR   0.008   0.001   TYR B 454 
 ARG   0.005   0.000   ARG A 131 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 1.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 MET cc_start: 0.8078 (mmt) cc_final: 0.7524 (mmm)
REVERT: A  323 ASN cc_start: 0.9486 (m110) cc_final: 0.9191 (p0)
REVERT: A  389 MET cc_start: 0.8736 (tmm) cc_final: 0.8218 (tmm)
REVERT: A  456 CYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6935 (t)
REVERT: A  680 MET cc_start: 0.8536 (ptt) cc_final: 0.8275 (pmm)
REVERT: A  698 MET cc_start: 0.9446 (mpp) cc_final: 0.9165 (mpp)
REVERT: A  717 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9326 (mt)
REVERT: A  772 MET cc_start: 0.8401 (mtp) cc_final: 0.8199 (mtp)
REVERT: B   43 MET cc_start: 0.0844 (mtp) cc_final: 0.0578 (mpp)
REVERT: B  177 PHE cc_start: 0.9189 (m-10) cc_final: 0.8915 (m-10)
REVERT: B  253 PHE cc_start: 0.8227 (m-80) cc_final: 0.7959 (m-80)
REVERT: B  273 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6840 (mmt)
REVERT: B  542 MET cc_start: 0.9189 (ptt) cc_final: 0.8815 (ptt)
REVERT: B  545 MET cc_start: 0.9168 (tmm) cc_final: 0.8831 (tmm)
REVERT: B  772 MET cc_start: 0.9597 (mtm) cc_final: 0.9098 (ptp)
REVERT: B  795 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8892 (mm)
REVERT: B  799 MET cc_start: 0.8927 (ttt) cc_final: 0.8433 (ptm)
  outliers start: 25
  outliers final: 20
  residues processed: 89
  average time/residue: 0.1954
  time to fit residues: 28.2739
Evaluate side-chains
  93 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  273 MET
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  795 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 142 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 89 optimal weight:    9.9990
   chunk 116 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   chunk 79 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.066395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.043655 restraints weight = 99817.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.044088 restraints weight = 78468.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.043634 restraints weight = 60105.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.4339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  12817  Z= 0.261
  Angle     :  0.742  10.650  17388  Z= 0.364
  Chirality :  0.044   0.161   1922
  Planarity :  0.005   0.048   2261
  Dihedral  :  5.951  70.429   1707
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.47 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.22), residues: 1562
  helix:  0.71 (0.20), residues: 719
  sheet: -0.56 (0.28), residues: 330
  loop : -0.98 (0.30), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 665 
 HIS   0.006   0.001   HIS B 663 
 PHE   0.023   0.002   PHE A 602 
 TYR   0.011   0.001   TYR B 415 
 ARG   0.005   0.000   ARG A 131 

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 1.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 MET cc_start: 0.8135 (mmt) cc_final: 0.7744 (mmm)
REVERT: A  323 ASN cc_start: 0.9395 (m110) cc_final: 0.9182 (p0)
REVERT: A  389 MET cc_start: 0.8730 (tmm) cc_final: 0.8174 (tmm)
REVERT: A  456 CYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6356 (t)
REVERT: A  680 MET cc_start: 0.8630 (ptt) cc_final: 0.8302 (pmm)
REVERT: A  698 MET cc_start: 0.9421 (mpp) cc_final: 0.9131 (mpp)
REVERT: A  717 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9351 (mt)
REVERT: B  273 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7152 (mmt)
REVERT: B  491 MET cc_start: 0.9248 (tpp) cc_final: 0.8596 (tpp)
REVERT: B  542 MET cc_start: 0.9073 (ptt) cc_final: 0.8714 (ptt)
REVERT: B  545 MET cc_start: 0.9190 (tmm) cc_final: 0.8865 (tmm)
REVERT: B  772 MET cc_start: 0.9599 (mtm) cc_final: 0.9126 (ptp)
REVERT: B  795 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8871 (mm)
REVERT: B  799 MET cc_start: 0.8887 (ttt) cc_final: 0.8420 (ptm)
  outliers start: 27
  outliers final: 16
  residues processed: 91
  average time/residue: 0.2039
  time to fit residues: 30.5622
Evaluate side-chains
  87 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  273 MET
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  795 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 88 optimal weight:    8.9990
   chunk 147 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 100 optimal weight:    0.0000
   chunk 139 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.7992

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.066053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.043260 restraints weight = 99442.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.042571 restraints weight = 76596.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.043104 restraints weight = 59745.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  12817  Z= 0.262
  Angle     :  0.744  10.849  17388  Z= 0.365
  Chirality :  0.045   0.434   1922
  Planarity :  0.005   0.048   2261
  Dihedral  :  5.962  70.466   1707
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.06 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.22), residues: 1562
  helix:  0.69 (0.20), residues: 719
  sheet: -0.61 (0.28), residues: 329
  loop : -0.96 (0.30), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 665 
 HIS   0.006   0.001   HIS B 663 
 PHE   0.022   0.002   PHE A 602 
 TYR   0.010   0.001   TYR B 415 
 ARG   0.005   0.000   ARG A 131 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3907.79 seconds
wall clock time: 72 minutes 8.13 seconds (4328.13 seconds total)