Starting phenix.real_space_refine
on Wed Jun 11 10:02:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ce0_45489/06_2025/9ce0_45489_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ce0_45489/06_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_45489/06_2025/9ce0_45489.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ce0_45489/06_2025/9ce0_45489.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ce0_45489/06_2025/9ce0_45489_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ce0_45489/06_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-5710/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: 7.37, per 1000 atoms: 0.59
  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: 3.09
  Conformation dependent library (CDL) restraints added in 1.5 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: 1.45
  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: 4.41

  Time building geometry restraints manager: 3.67 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:             30.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     30.160
  Find NCS groups from input model:        0.510
  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:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.470
-------------------------------------------------------------------------------
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      :  0.010   0.714  12819  Z= 0.233
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10649 (  688)
  hydrogen bonds       : angle       6.47419 ( 1998)
  covalent geometry    : bond        0.00412 (12817)
  covalent geometry    : angle       0.69275 (17388)
  Misc. bond           : bond        0.70627 (    2)

*********************** 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  : 1.251 
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: 0.3020
  time to fit residues: 59.4445
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  : 1.417 
-------------------------------------------------------------------------------
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 = 0.070103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.046697 restraints weight = 92197.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.046184 restraints weight = 72583.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.046693 restraints weight = 58640.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
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   0.265  12819  Z= 0.161
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04530 (  688)
  hydrogen bonds       : angle       5.63599 ( 1998)
  covalent geometry    : bond        0.00360 (12817)
  covalent geometry    : angle       0.74819 (17388)
  Misc. bond           : bond        0.20576 (    2)

*********************** 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  : 1.292 
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: -0.3144 (t80) cc_final: -0.3591 (t80)
REVERT: A  343 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.9091 (tm-30)
REVERT: A  682 MET cc_start: 0.9018 (mmm) cc_final: 0.8676 (mmm)
REVERT: B  253 PHE cc_start: 0.8617 (m-80) cc_final: 0.8219 (m-10)
REVERT: B  282 MET cc_start: 0.8225 (mtt) cc_final: 0.8008 (mpp)
REVERT: B  772 MET cc_start: 0.9325 (mtm) cc_final: 0.9026 (ptp)
  outliers start: 21
  outliers final: 5
  residues processed: 106
  average time/residue: 0.2509
  time to fit residues: 39.3536
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  : 1.504 
-------------------------------------------------------------------------------
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:    8.9990
   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:    1.9990
   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:    3.1388

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.066261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.043221 restraints weight = 98701.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.042780 restraints weight = 79257.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.043289 restraints weight = 63243.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.316  12819  Z= 0.306
  Angle     :  0.789   8.329  17388  Z= 0.407
  Chirality :  0.047   0.163   1922
  Planarity :  0.006   0.059   2261
  Dihedral  :  6.430  70.827   1707
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 18.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.31 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.46 %
    Favored  : 83.68 %
  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: -0.88 (0.21), residues: 1562
  helix:  0.16 (0.19), residues: 709
  sheet: -0.79 (0.28), residues: 340
  loop : -1.28 (0.29), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   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   0.007   0.001   ARG A 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04580 (  688)
  hydrogen bonds       : angle       5.87870 ( 1998)
  covalent geometry    : bond        0.00631 (12817)
  covalent geometry    : angle       0.78913 (17388)
  Misc. bond           : bond        0.22391 (    2)

*********************** 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
  114 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 75
  time to evaluate  : 1.443 
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: A  176 MET cc_start: 0.8157 (ttt) cc_final: 0.7893 (ptm)
REVERT: A  389 MET cc_start: 0.8687 (tmm) cc_final: 0.8256 (tmm)
REVERT: A  682 MET cc_start: 0.9388 (mmm) cc_final: 0.9025 (mmm)
REVERT: A  698 MET cc_start: 0.9411 (mpp) cc_final: 0.8957 (mpp)
REVERT: A  772 MET cc_start: 0.8626 (mtp) cc_final: 0.8382 (mtp)
REVERT: B  282 MET cc_start: 0.8242 (mtt) cc_final: 0.7968 (ptp)
REVERT: B  682 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8190 (mmm)
REVERT: B  772 MET cc_start: 0.9546 (mtm) cc_final: 0.9161 (ptp)
REVERT: B  799 MET cc_start: 0.9234 (ttt) cc_final: 0.8269 (ppp)
  outliers start: 39
  outliers final: 15
  residues processed: 108
  average time/residue: 0.3125
  time to fit residues: 51.8468
Evaluate side-chains
  89 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 2.339 
-------------------------------------------------------------------------------
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  205 ARG
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  682 MET
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:    1.9990
   chunk 1 optimal weight:   30.0000
   chunk 0 optimal weight:   40.0000
   chunk 127 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 108 optimal weight:    8.9990
   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 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 = 0.3705 r_free = 0.3705 target = 0.066847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.043598 restraints weight = 95707.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.042968 restraints weight = 75772.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.043313 restraints weight = 61830.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.250  12819  Z= 0.190
  Angle     :  0.704   9.896  17388  Z= 0.355
  Chirality :  0.044   0.155   1922
  Planarity :  0.005   0.046   2261
  Dihedral  :  6.294  68.336   1707
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.25 %
    Favored  : 94.62 %
  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: -0.67 (0.22), residues: 1562
  helix:  0.42 (0.19), residues: 705
  sheet: -0.77 (0.28), residues: 341
  loop : -1.25 (0.29), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 665 
 HIS   0.006   0.001   HIS A  77 
 PHE   0.024   0.002   PHE A 602 
 TYR   0.014   0.001   TYR B 454 
 ARG   0.014   0.001   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  688)
  hydrogen bonds       : angle       5.53852 ( 1998)
  covalent geometry    : bond        0.00407 (12817)
  covalent geometry    : angle       0.70440 (17388)
  Misc. bond           : bond        0.17705 (    2)

*********************** 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
  107 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 72
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9778 (tpp) cc_final: 0.9559 (mmm)
REVERT: A  389 MET cc_start: 0.8698 (tmm) cc_final: 0.8248 (tmm)
REVERT: A  682 MET cc_start: 0.9376 (mmm) cc_final: 0.9161 (mmm)
REVERT: A  698 MET cc_start: 0.9421 (mpp) cc_final: 0.8950 (mpp)
REVERT: A  758 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8717 (p)
REVERT: A  772 MET cc_start: 0.8559 (mtp) cc_final: 0.8320 (mtp)
REVERT: B  139 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8825 (tm-30)
REVERT: B  542 MET cc_start: 0.9170 (ptt) cc_final: 0.8786 (ptt)
REVERT: B  545 MET cc_start: 0.9165 (tmm) cc_final: 0.8856 (tmm)
REVERT: B  772 MET cc_start: 0.9585 (mtm) cc_final: 0.9160 (ptp)
  outliers start: 35
  outliers final: 19
  residues processed: 102
  average time/residue: 0.3068
  time to fit residues: 49.4609
Evaluate side-chains
  91 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 1.721 
-------------------------------------------------------------------------------
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  758 THR
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 ARG
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:    0.7980
   chunk 121 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 52 optimal weight:    0.4980
   chunk 138 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 126 optimal weight:    4.9990
   chunk 8 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 ** 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 = 0.3717 r_free = 0.3717 target = 0.067333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.043322 restraints weight = 97050.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.042666 restraints weight = 75697.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.043159 restraints weight = 61757.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.265  12819  Z= 0.152
  Angle     :  0.693   9.590  17388  Z= 0.345
  Chirality :  0.044   0.211   1922
  Planarity :  0.005   0.056   2261
  Dihedral  :  6.170  68.391   1707
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.38 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.49 %
    Favored  : 82.94 %
  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: -0.51 (0.22), residues: 1562
  helix:  0.58 (0.20), residues: 709
  sheet: -0.69 (0.28), residues: 333
  loop : -1.22 (0.29), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 231 
 HIS   0.004   0.001   HIS A  77 
 PHE   0.024   0.002   PHE A 602 
 TYR   0.010   0.001   TYR B 454 
 ARG   0.004   0.000   ARG A 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  688)
  hydrogen bonds       : angle       5.41439 ( 1998)
  covalent geometry    : bond        0.00335 (12817)
  covalent geometry    : angle       0.69301 (17388)
  Misc. bond           : bond        0.18798 (    2)

*********************** 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
  109 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 74
  time to evaluate  : 1.359 
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: A  323 ASN cc_start: 0.9585 (m110) cc_final: 0.9278 (p0)
REVERT: A  389 MET cc_start: 0.8680 (tmm) cc_final: 0.8217 (tmm)
REVERT: A  456 CYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7088 (t)
REVERT: A  682 MET cc_start: 0.9374 (mmm) cc_final: 0.9163 (mmm)
REVERT: A  717 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9271 (mt)
REVERT: A  758 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8688 (p)
REVERT: A  772 MET cc_start: 0.8536 (mtp) cc_final: 0.8303 (mtp)
REVERT: B   30 MET cc_start: -0.2939 (tpt) cc_final: -0.3329 (tpt)
REVERT: B  177 PHE cc_start: 0.9700 (m-80) cc_final: 0.9177 (m-80)
REVERT: B  282 MET cc_start: 0.8565 (ptp) cc_final: 0.8358 (mpp)
REVERT: B  542 MET cc_start: 0.9187 (ptt) cc_final: 0.8789 (ptt)
REVERT: B  545 MET cc_start: 0.9178 (tmm) cc_final: 0.8849 (tmm)
REVERT: B  772 MET cc_start: 0.9610 (mtm) cc_final: 0.9160 (ptp)
REVERT: B  787 SER cc_start: 0.9275 (OUTLIER) cc_final: 0.8913 (p)
REVERT: B  795 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8752 (mm)
  outliers start: 35
  outliers final: 19
  residues processed: 103
  average time/residue: 0.2628
  time to fit residues: 42.1898
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  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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   31 MET
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 ARG
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
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:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 108 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:   20.0000
   chunk 146 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 36 optimal weight:    0.2980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 653 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.066883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.043473 restraints weight = 98559.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.042764 restraints weight = 77826.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.043283 restraints weight = 63154.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.272  12819  Z= 0.163
  Angle     :  0.711  12.512  17388  Z= 0.351
  Chirality :  0.044   0.164   1922
  Planarity :  0.005   0.050   2261
  Dihedral  :  6.104  68.003   1707
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.38 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.07 %
    Favored  : 82.35 %
  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: -0.41 (0.22), residues: 1562
  helix:  0.65 (0.19), residues: 718
  sheet: -0.67 (0.28), residues: 322
  loop : -1.15 (0.29), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 665 
 HIS   0.004   0.001   HIS A  77 
 PHE   0.023   0.002   PHE A 602 
 TYR   0.014   0.001   TYR B 125 
 ARG   0.004   0.000   ARG B  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  688)
  hydrogen bonds       : angle       5.34929 ( 1998)
  covalent geometry    : bond        0.00356 (12817)
  covalent geometry    : angle       0.71118 (17388)
  Misc. bond           : bond        0.19401 (    2)

*********************** 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
  108 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 73
  time to evaluate  : 1.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 MET cc_start: 0.8762 (tmm) cc_final: 0.8214 (tmm)
REVERT: A  456 CYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7230 (t)
REVERT: A  681 MET cc_start: 0.9374 (tpp) cc_final: 0.9095 (tpp)
REVERT: A  698 MET cc_start: 0.9405 (mpp) cc_final: 0.9147 (mpp)
REVERT: A  717 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9332 (mt)
REVERT: A  758 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8771 (p)
REVERT: A  772 MET cc_start: 0.8511 (mtp) cc_final: 0.8289 (mtp)
REVERT: B  139 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8701 (tm-30)
REVERT: B  253 PHE cc_start: 0.8477 (m-10) cc_final: 0.8253 (m-80)
REVERT: B  419 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8473 (p)
REVERT: B  542 MET cc_start: 0.9175 (ptt) cc_final: 0.8778 (ptt)
REVERT: B  545 MET cc_start: 0.9185 (tmm) cc_final: 0.8858 (tmm)
REVERT: B  680 MET cc_start: 0.9254 (ttt) cc_final: 0.9049 (ttt)
REVERT: B  772 MET cc_start: 0.9590 (mtm) cc_final: 0.9110 (ptp)
REVERT: B  787 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.8948 (p)
REVERT: B  795 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8870 (mm)
REVERT: B  799 MET cc_start: 0.9072 (ttt) cc_final: 0.8217 (ppp)
  outliers start: 35
  outliers final: 22
  residues processed: 102
  average time/residue: 0.2103
  time to fit residues: 33.6341
Evaluate side-chains
  101 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
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  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 A residue  758 THR
Chi-restraints excluded: chain B residue  139 GLN
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  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  787 SER
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:    7.9990
   chunk 90 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 122 optimal weight:    0.0010
   chunk 145 optimal weight:    0.0980
   chunk 137 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.0190

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.067250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.043950 restraints weight = 97722.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.043224 restraints weight = 76799.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.043635 restraints weight = 62100.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.259  12819  Z= 0.140
  Angle     :  0.690   9.207  17388  Z= 0.341
  Chirality :  0.043   0.153   1922
  Planarity :  0.005   0.053   2261
  Dihedral  :  6.007  68.549   1707
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.96 %
    Favored  : 81.84 %
  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: -0.33 (0.22), residues: 1562
  helix:  0.70 (0.20), residues: 714
  sheet: -0.59 (0.28), residues: 320
  loop : -1.09 (0.29), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  53 
 HIS   0.004   0.001   HIS A  77 
 PHE   0.023   0.002   PHE A 602 
 TYR   0.008   0.001   TYR B 454 
 ARG   0.003   0.000   ARG A 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  688)
  hydrogen bonds       : angle       5.25648 ( 1998)
  covalent geometry    : bond        0.00308 (12817)
  covalent geometry    : angle       0.69033 (17388)
  Misc. bond           : bond        0.18471 (    2)

*********************** 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
  103 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 2.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASN cc_start: 0.9430 (m110) cc_final: 0.9146 (p0)
REVERT: A  389 MET cc_start: 0.8785 (tmm) cc_final: 0.8234 (tmm)
REVERT: A  680 MET cc_start: 0.8607 (ptt) cc_final: 0.8261 (pmm)
REVERT: A  698 MET cc_start: 0.9478 (mpp) cc_final: 0.9199 (mpp)
REVERT: A  717 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9360 (mt)
REVERT: A  758 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8708 (p)
REVERT: A  772 MET cc_start: 0.8480 (mtp) cc_final: 0.8259 (mtp)
REVERT: B  139 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8726 (tm-30)
REVERT: B  419 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8433 (p)
REVERT: B  542 MET cc_start: 0.9192 (ptt) cc_final: 0.8800 (ptt)
REVERT: B  545 MET cc_start: 0.9154 (tmm) cc_final: 0.8806 (tmm)
REVERT: B  772 MET cc_start: 0.9609 (mtm) cc_final: 0.9120 (ptp)
REVERT: B  787 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.8788 (p)
REVERT: B  795 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8895 (mm)
REVERT: B  799 MET cc_start: 0.9063 (ttt) cc_final: 0.8517 (ptm)
  outliers start: 30
  outliers final: 19
  residues processed: 98
  average time/residue: 0.2216
  time to fit residues: 36.4061
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  : 1.456 
-------------------------------------------------------------------------------
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  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  222 LEU
Chi-restraints excluded: chain B residue  239 VAL
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
Chi-restraints excluded: chain B residue  787 SER
Chi-restraints excluded: chain B residue  795 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 6 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 99 optimal weight:    7.9990
   chunk 106 optimal weight:    9.9990
   chunk 78 optimal weight:    0.0030
   chunk 41 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    2.7996

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

Flipped N/Q/H residues before XYZ refinement:
** A 168 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 = 0.3664 r_free = 0.3664 target = 0.064796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.042014 restraints weight = 101176.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.041446 restraints weight = 77596.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.041894 restraints weight = 62260.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.257  12819  Z= 0.268
  Angle     :  0.792   9.857  17388  Z= 0.397
  Chirality :  0.045   0.156   1922
  Planarity :  0.006   0.062   2261
  Dihedral  :  6.181  66.123   1707
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.32 %
    Favored  : 80.96 %
  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: -0.67 (0.21), residues: 1562
  helix:  0.40 (0.19), residues: 716
  sheet: -0.83 (0.28), residues: 322
  loop : -1.18 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 665 
 HIS   0.008   0.002   HIS A 596 
 PHE   0.027   0.002   PHE A 602 
 TYR   0.018   0.002   TYR A 569 
 ARG   0.005   0.001   ARG B 650 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  688)
  hydrogen bonds       : angle       5.63742 ( 1998)
  covalent geometry    : bond        0.00566 (12817)
  covalent geometry    : angle       0.79227 (17388)
  Misc. bond           : bond        0.19316 (    2)

*********************** 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
  106 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 69
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASN cc_start: 0.9400 (m110) cc_final: 0.9179 (p0)
REVERT: A  389 MET cc_start: 0.8891 (tmm) cc_final: 0.8318 (tmm)
REVERT: A  456 CYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5547 (t)
REVERT: A  698 MET cc_start: 0.9429 (mpp) cc_final: 0.9117 (mpp)
REVERT: A  758 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8759 (p)
REVERT: A  772 MET cc_start: 0.8611 (mtp) cc_final: 0.8385 (mtp)
REVERT: B  139 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8932 (tm-30)
REVERT: B  542 MET cc_start: 0.9119 (ptt) cc_final: 0.8755 (ptt)
REVERT: B  545 MET cc_start: 0.9203 (tmm) cc_final: 0.8870 (tmm)
REVERT: B  772 MET cc_start: 0.9609 (mtm) cc_final: 0.9179 (ptp)
REVERT: B  795 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8974 (mm)
REVERT: B  799 MET cc_start: 0.9066 (ttt) cc_final: 0.8282 (ppp)
  outliers start: 37
  outliers final: 23
  residues processed: 102
  average time/residue: 0.2054
  time to fit residues: 33.7468
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  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 THR
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  285 ILE
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  635 ILE
Chi-restraints excluded: chain A residue  654 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  222 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0980
   chunk 154 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 134 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 168 GLN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.066616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.043790 restraints weight = 99124.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.044043 restraints weight = 77375.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.043632 restraints weight = 59339.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.222  12819  Z= 0.142
  Angle     :  0.733  10.692  17388  Z= 0.358
  Chirality :  0.044   0.153   1922
  Planarity :  0.005   0.049   2261
  Dihedral  :  6.068  67.990   1707
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.57 %
    Favored  : 80.59 %
  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: -0.33 (0.22), residues: 1562
  helix:  0.68 (0.20), residues: 713
  sheet: -0.67 (0.29), residues: 316
  loop : -1.02 (0.29), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 110 
 HIS   0.007   0.001   HIS B 298 
 PHE   0.023   0.002   PHE A 602 
 TYR   0.007   0.001   TYR B 454 
 ARG   0.010   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03573 (  688)
  hydrogen bonds       : angle       5.37120 ( 1998)
  covalent geometry    : bond        0.00319 (12817)
  covalent geometry    : angle       0.73337 (17388)
  Misc. bond           : bond        0.16055 (    2)

*********************** 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
  93 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 1.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASN cc_start: 0.9482 (m110) cc_final: 0.9230 (p0)
REVERT: A  389 MET cc_start: 0.8815 (tmm) cc_final: 0.8229 (tmm)
REVERT: A  680 MET cc_start: 0.8492 (ptt) cc_final: 0.8256 (pmm)
REVERT: A  681 MET cc_start: 0.9184 (tpp) cc_final: 0.8880 (tpp)
REVERT: A  698 MET cc_start: 0.9434 (mpp) cc_final: 0.9093 (mpp)
REVERT: A  772 MET cc_start: 0.8547 (mtp) cc_final: 0.8340 (mtp)
REVERT: B  139 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8895 (tm-30)
REVERT: B  491 MET cc_start: 0.9074 (tpp) cc_final: 0.8327 (tpp)
REVERT: B  542 MET cc_start: 0.9161 (ptt) cc_final: 0.8781 (ptt)
REVERT: B  545 MET cc_start: 0.9151 (tmm) cc_final: 0.8765 (tmm)
REVERT: B  772 MET cc_start: 0.9600 (mtm) cc_final: 0.9130 (ptp)
REVERT: B  787 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.8698 (p)
REVERT: B  799 MET cc_start: 0.8926 (ttt) cc_final: 0.8433 (ptm)
  outliers start: 25
  outliers final: 20
  residues processed: 89
  average time/residue: 0.2193
  time to fit residues: 31.7939
Evaluate side-chains
  90 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 VAL
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  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  258 GLU
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  787 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 142 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0470
   chunk 89 optimal weight:    9.9990
   chunk 116 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 101 optimal weight:    3.9990
   chunk 84 optimal weight:    9.9990
   chunk 79 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.8086

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.065597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.042392 restraints weight = 99866.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.041545 restraints weight = 78828.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.041994 restraints weight = 63165.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.208  12819  Z= 0.193
  Angle     :  0.764  11.010  17388  Z= 0.378
  Chirality :  0.045   0.259   1922
  Planarity :  0.005   0.047   2261
  Dihedral  :  6.087  68.264   1707
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 18.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.79 %
    Favored  : 80.44 %
  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: -0.39 (0.22), residues: 1562
  helix:  0.62 (0.20), residues: 713
  sheet: -0.71 (0.29), residues: 316
  loop : -1.01 (0.29), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 665 
 HIS   0.005   0.001   HIS B 298 
 PHE   0.025   0.002   PHE A 602 
 TYR   0.012   0.001   TYR A 569 
 ARG   0.005   0.001   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03642 (  688)
  hydrogen bonds       : angle       5.42146 ( 1998)
  covalent geometry    : bond        0.00421 (12817)
  covalent geometry    : angle       0.76352 (17388)
  Misc. bond           : bond        0.15252 (    2)

********************** 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
  89 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 65
  time to evaluate  : 1.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASN cc_start: 0.9524 (m110) cc_final: 0.9270 (p0)
REVERT: A  389 MET cc_start: 0.8868 (tmm) cc_final: 0.8275 (tmm)
REVERT: A  681 MET cc_start: 0.9206 (tpp) cc_final: 0.8735 (tpp)
REVERT: A  698 MET cc_start: 0.9442 (mpp) cc_final: 0.9105 (mpp)
REVERT: A  772 MET cc_start: 0.8588 (mtp) cc_final: 0.8371 (mtp)
REVERT: B  139 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8910 (tm-30)
REVERT: B  491 MET cc_start: 0.9293 (tpp) cc_final: 0.8664 (tpp)
REVERT: B  542 MET cc_start: 0.9123 (ptt) cc_final: 0.8754 (ptt)
REVERT: B  545 MET cc_start: 0.9201 (tmm) cc_final: 0.8853 (tmm)
REVERT: B  772 MET cc_start: 0.9622 (mtm) cc_final: 0.9177 (ptp)
REVERT: B  787 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.8614 (p)
REVERT: B  799 MET cc_start: 0.8915 (ttt) cc_final: 0.8467 (ptm)
  outliers start: 24
  outliers final: 21
  residues processed: 87
  average time/residue: 0.1873
  time to fit residues: 26.9198
Evaluate side-chains
  88 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 VAL
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  472 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  258 GLU
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  787 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 147 optimal weight:    0.4980
   chunk 101 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   chunk 139 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 123 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.066368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.043452 restraints weight = 98478.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.042403 restraints weight = 78555.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.042883 restraints weight = 61686.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.198  12819  Z= 0.144
  Angle     :  0.746   9.955  17388  Z= 0.364
  Chirality :  0.044   0.260   1922
  Planarity :  0.005   0.048   2261
  Dihedral  :  6.046  69.653   1707
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 17.50 %
    Favored  : 80.81 %
  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: -0.32 (0.22), residues: 1562
  helix:  0.68 (0.20), residues: 714
  sheet: -0.65 (0.29), residues: 321
  loop : -1.01 (0.29), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 110 
 HIS   0.004   0.001   HIS A 521 
 PHE   0.023   0.002   PHE A 602 
 TYR   0.008   0.001   TYR B 454 
 ARG   0.005   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03440 (  688)
  hydrogen bonds       : angle       5.30719 ( 1998)
  covalent geometry    : bond        0.00324 (12817)
  covalent geometry    : angle       0.74650 (17388)
  Misc. bond           : bond        0.14128 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4878.96 seconds
wall clock time: 87 minutes 47.80 seconds (5267.80 seconds total)