Starting phenix.real_space_refine
on Thu May  9 02:56:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/05_2024/8rfh_19121_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/05_2024/8rfh_19121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/05_2024/8rfh_19121.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/05_2024/8rfh_19121.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/05_2024/8rfh_19121_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/05_2024/8rfh_19121_updated.pdb"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 54 atoms to isotropic.
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
     P       4      5.49       5
     S      58      5.16       5
     C    7550      2.51       5
     N    2032      2.21       5
     O    2158      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  243": "OE1" <-> "OE2"
    Residue "A GLU  273": "OE1" <-> "OE2"
    Residue "A TYR  413": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  490": "OE1" <-> "OE2"
    Residue "A GLU  610": "OE1" <-> "OE2"
    Residue "B GLU  243": "OE1" <-> "OE2"
    Residue "B GLU  273": "OE1" <-> "OE2"
    Residue "B ASP  317": "OD1" <-> "OD2"
    Residue "B TYR  413": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  490": "OE1" <-> "OE2"
    Residue "B GLU  610": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib"
  Total number of atoms: 11802
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 730, 5874
          Classifications: {'peptide': 730}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 730, 5874
          Classifications: {'peptide': 730}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.42, per 1000 atoms: 0.54
  Number of scatterers: 11802
  At special positions: 0
  Unit cell: (141.588, 78.66, 91.908, 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)
     S      58     16.00
     P       4     15.00
     O    2158      8.00
     N    2032      7.00
     C    7550      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.66
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2752

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      60 helices and 12 sheets defined
      37.7% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 158 through 169
    Processing helix  chain 'A' and resid 188 through 197
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 3.575A  pdb=" N   LYS A 229 " --> pdb=" O   ASN A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 269 through 278
      removed outlier: 3.943A  pdb=" N   ILE A 277 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   ALA A 278 " --> pdb=" O   ARG A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 300
    Processing helix  chain 'A' and resid 316 through 327
      removed outlier: 3.550A  pdb=" N   ILE A 321 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 347
      removed outlier: 4.111A  pdb=" N   LEU A 339 " --> pdb=" O   PRO A 335 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   SER A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 365
    Processing helix  chain 'A' and resid 369 through 381
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 4.730A  pdb=" N   ASP A 401 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 416
      removed outlier: 3.688A  pdb=" N   GLY A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ALA A 416 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 434
    Processing helix  chain 'A' and resid 446 through 459
    Processing helix  chain 'A' and resid 481 through 493
    Processing helix  chain 'A' and resid 512 through 517
      removed outlier: 4.313A  pdb=" N   THR A 517 " --> pdb=" O   ARG A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 533
    Processing helix  chain 'A' and resid 555 through 564
      Proline residue:  A 559  - end of helix
      Proline residue:  A 562  - end of helix
      No H-bonds generated for 'chain 'A' and resid 555 through 564'
    Processing helix  chain 'A' and resid 584 through 587
    Processing helix  chain 'A' and resid 606 through 610
    Processing helix  chain 'A' and resid 675 through 677
      No H-bonds generated for 'chain 'A' and resid 675 through 677'
    Processing helix  chain 'A' and resid 680 through 684
    Processing helix  chain 'A' and resid 698 through 701
      No H-bonds generated for 'chain 'A' and resid 698 through 701'
    Processing helix  chain 'A' and resid 708 through 714
    Processing helix  chain 'A' and resid 739 through 741
      No H-bonds generated for 'chain 'A' and resid 739 through 741'
    Processing helix  chain 'A' and resid 758 through 766
    Processing helix  chain 'A' and resid 833 through 837
    Processing helix  chain 'A' and resid 851 through 870
    Processing helix  chain 'B' and resid 158 through 169
    Processing helix  chain 'B' and resid 188 through 197
    Processing helix  chain 'B' and resid 199 through 204
    Processing helix  chain 'B' and resid 219 through 229
      removed outlier: 3.575A  pdb=" N   LYS B 229 " --> pdb=" O   ASN B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 237
      No H-bonds generated for 'chain 'B' and resid 235 through 237'
    Processing helix  chain 'B' and resid 242 through 255
    Processing helix  chain 'B' and resid 269 through 278
      removed outlier: 3.943A  pdb=" N   ILE B 277 " --> pdb=" O   GLU B 273 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   ALA B 278 " --> pdb=" O   ARG B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 300
    Processing helix  chain 'B' and resid 316 through 327
    Processing helix  chain 'B' and resid 335 through 347
      removed outlier: 4.111A  pdb=" N   LEU B 339 " --> pdb=" O   PRO B 335 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   SER B 340 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 365
    Processing helix  chain 'B' and resid 369 through 381
    Processing helix  chain 'B' and resid 390 through 402
      removed outlier: 3.779A  pdb=" N   LYS B 394 " --> pdb=" O   GLU B 390 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 395 " --> pdb=" O   ASN B 391 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   ARG B 402 " --> pdb=" O   LEU B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 416
      removed outlier: 3.687A  pdb=" N   GLY B 415 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ALA B 416 " --> pdb=" O   LEU B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 435
    Processing helix  chain 'B' and resid 446 through 459
    Processing helix  chain 'B' and resid 481 through 493
    Processing helix  chain 'B' and resid 512 through 517
      removed outlier: 4.313A  pdb=" N   THR B 517 " --> pdb=" O   ARG B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 533
    Processing helix  chain 'B' and resid 555 through 564
      Proline residue:  B 559  - end of helix
      Proline residue:  B 562  - end of helix
      No H-bonds generated for 'chain 'B' and resid 555 through 564'
    Processing helix  chain 'B' and resid 584 through 587
    Processing helix  chain 'B' and resid 606 through 610
    Processing helix  chain 'B' and resid 675 through 677
      No H-bonds generated for 'chain 'B' and resid 675 through 677'
    Processing helix  chain 'B' and resid 680 through 684
    Processing helix  chain 'B' and resid 698 through 701
      No H-bonds generated for 'chain 'B' and resid 698 through 701'
    Processing helix  chain 'B' and resid 708 through 714
    Processing helix  chain 'B' and resid 739 through 741
      No H-bonds generated for 'chain 'B' and resid 739 through 741'
    Processing helix  chain 'B' and resid 758 through 766
    Processing helix  chain 'B' and resid 833 through 837
    Processing helix  chain 'B' and resid 851 through 870
    Processing sheet with id=  A, first strand: chain 'A' and resid 176 through 181
      removed outlier: 6.466A  pdb=" N   THR A 207 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   VAL A 262 " --> pdb=" O   THR A 207 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   ILE A 209 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   ASP A 264 " --> pdb=" O   ILE A 209 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   VAL A 211 " --> pdb=" O   ASP A 264 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 499 through 501
      removed outlier: 3.587A  pdb=" N   GLN A 499 " --> pdb=" O   ARG A 520 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   CYS A 522 " --> pdb=" O   GLN A 499 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE A 501 " --> pdb=" O   CYS A 522 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   SER A 542 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   ILE A 523 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LEU A 544 " --> pdb=" O   ILE A 523 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   VAL A 570 " --> pdb=" O   PHE A 543 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   TYR A 593 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL A 573 " --> pdb=" O   TYR A 593 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ALA A 595 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   SER A 575 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   SER A 597 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ASN A 577 " --> pdb=" O   SER A 597 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   THR A 616 " --> pdb=" O   ILE A 594 " (cutoff:3.500A)
      removed outlier: 8.688A  pdb=" N   PHE A 596 " --> pdb=" O   THR A 616 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ILE A 618 " --> pdb=" O   PHE A 596 " (cutoff:3.500A)
      removed outlier: 8.251A  pdb=" N   SER A 598 " --> pdb=" O   ILE A 618 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ASN A 620 " --> pdb=" O   SER A 598 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   HIS A 640 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   ILE A 619 " --> pdb=" O   HIS A 640 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   HIS A 642 " --> pdb=" O   ILE A 619 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   THR A 621 " --> pdb=" O   HIS A 642 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  B
    Processing sheet with id=  C, first strand: chain 'A' and resid 625 through 627
      removed outlier: 5.819A  pdb=" N   SER A 646 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C
    Processing sheet with id=  D, first strand: chain 'A' and resid 843 through 845
      removed outlier: 3.715A  pdb=" N   GLU A 845 " --> pdb=" O   LEU A 820 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 822 " --> pdb=" O   GLU A 845 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU A 749 " --> pdb=" O   VAL A 772 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS A 774 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A 752 " --> pdb=" O   LEU A 723 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN A 725 " --> pdb=" O   VAL A 752 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   THR A 672 " --> pdb=" O   GLY A 693 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   ARG A 695 " --> pdb=" O   THR A 672 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 784 through 786
      removed outlier: 6.478A  pdb=" N   SER A 806 " --> pdb=" O   TRP A 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  E
    Processing sheet with id=  F, first strand: chain 'A' and resid 463 through 467
      removed outlier: 6.826A  pdb=" N   THR A 476 " --> pdb=" O   MET A 466 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 176 through 181
      removed outlier: 6.466A  pdb=" N   THR B 207 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   VAL B 262 " --> pdb=" O   THR B 207 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   ILE B 209 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   ASP B 264 " --> pdb=" O   ILE B 209 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   VAL B 211 " --> pdb=" O   ASP B 264 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 499 through 501
      removed outlier: 3.585A  pdb=" N   GLN B 499 " --> pdb=" O   ARG B 520 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   CYS B 522 " --> pdb=" O   GLN B 499 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ILE B 501 " --> pdb=" O   CYS B 522 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER B 542 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ILE B 523 " --> pdb=" O   SER B 542 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LEU B 544 " --> pdb=" O   ILE B 523 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   VAL B 570 " --> pdb=" O   PHE B 543 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   TYR B 593 " --> pdb=" O   PHE B 571 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL B 573 " --> pdb=" O   TYR B 593 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ALA B 595 " --> pdb=" O   VAL B 573 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   SER B 575 " --> pdb=" O   ALA B 595 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   SER B 597 " --> pdb=" O   SER B 575 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ASN B 577 " --> pdb=" O   SER B 597 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   THR B 616 " --> pdb=" O   ILE B 594 " (cutoff:3.500A)
      removed outlier: 8.689A  pdb=" N   PHE B 596 " --> pdb=" O   THR B 616 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ILE B 618 " --> pdb=" O   PHE B 596 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   SER B 598 " --> pdb=" O   ILE B 618 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ASN B 620 " --> pdb=" O   SER B 598 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   HIS B 640 " --> pdb=" O   LEU B 617 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   ILE B 619 " --> pdb=" O   HIS B 640 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   HIS B 642 " --> pdb=" O   ILE B 619 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   THR B 621 " --> pdb=" O   HIS B 642 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  H
    Processing sheet with id=  I, first strand: chain 'B' and resid 625 through 627
      removed outlier: 5.820A  pdb=" N   SER B 646 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  I
    Processing sheet with id=  J, first strand: chain 'B' and resid 843 through 845
      removed outlier: 3.714A  pdb=" N   GLU B 845 " --> pdb=" O   LEU B 820 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU B 822 " --> pdb=" O   GLU B 845 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU B 749 " --> pdb=" O   VAL B 772 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS B 774 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL B 752 " --> pdb=" O   LEU B 723 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASN B 725 " --> pdb=" O   VAL B 752 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR B 672 " --> pdb=" O   GLY B 693 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   ARG B 695 " --> pdb=" O   THR B 672 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'B' and resid 784 through 786
      removed outlier: 6.478A  pdb=" N   SER B 806 " --> pdb=" O   TRP B 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  K
    Processing sheet with id=  L, first strand: chain 'B' and resid 463 through 467
      removed outlier: 6.828A  pdb=" N   THR B 476 " --> pdb=" O   MET B 466 " (cutoff:3.500A)

    362 hydrogen bonds defined for protein.
    960 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: 3.98

  Time building geometry restraints manager: 4.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3588
        1.34 -     1.45: 1609
        1.45 -     1.57: 6771
        1.57 -     1.69: 6
        1.69 -     1.81: 82
  Bond restraints: 12056
  Sorted by residual:
  bond pdb=" N   THR A 315 "
       pdb=" CA  THR A 315 "
    ideal  model  delta    sigma   weight residual
    1.453  1.496 -0.043 1.31e-02 5.83e+03 1.08e+01
  bond pdb=" N   ILE A 673 "
       pdb=" CA  ILE A 673 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.14e-02 7.69e+03 1.05e+01
  bond pdb=" N   THR B 315 "
       pdb=" CA  THR B 315 "
    ideal  model  delta    sigma   weight residual
    1.454  1.496 -0.042 1.34e-02 5.57e+03 9.89e+00
  bond pdb=" N   LEU A 314 "
       pdb=" CA  LEU A 314 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.22e-02 6.72e+03 8.79e+00
  bond pdb=" N   ILE A 433 "
       pdb=" CA  ILE A 433 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.21e-02 6.83e+03 8.15e+00
  ... (remaining 12051 not shown)

  Histogram of bond angle deviations from ideal:
       97.92 -   105.52: 210
      105.52 -   113.12: 6681
      113.12 -   120.73: 5335
      120.73 -   128.33: 3961
      128.33 -   135.93: 99
  Bond angle restraints: 16286
  Sorted by residual:
  angle pdb=" C   SER A 671 "
        pdb=" N   THR A 672 "
        pdb=" CA  THR A 672 "
      ideal   model   delta    sigma   weight residual
     122.30  114.12    8.18 1.35e+00 5.49e-01 3.67e+01
  angle pdb=" C   THR A 672 "
        pdb=" CA  THR A 672 "
        pdb=" CB  THR A 672 "
      ideal   model   delta    sigma   weight residual
     110.22  120.17   -9.95 1.67e+00 3.59e-01 3.55e+01
  angle pdb=" N   ASP B 317 "
        pdb=" CA  ASP B 317 "
        pdb=" C   ASP B 317 "
      ideal   model   delta    sigma   weight residual
     111.28  105.88    5.40 1.09e+00 8.42e-01 2.46e+01
  angle pdb=" N   ASP A 317 "
        pdb=" CA  ASP A 317 "
        pdb=" C   ASP A 317 "
      ideal   model   delta    sigma   weight residual
     111.28  106.71    4.57 1.09e+00 8.42e-01 1.76e+01
  angle pdb=" C   GLU A 316 "
        pdb=" CA  GLU A 316 "
        pdb=" CB  GLU A 316 "
      ideal   model   delta    sigma   weight residual
     110.79  105.33    5.46 1.66e+00 3.63e-01 1.08e+01
  ... (remaining 16281 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.69: 7135
       34.69 -    69.38: 185
       69.38 -   104.07: 12
      104.07 -   138.76: 0
      138.76 -   173.45: 2
  Dihedral angle restraints: 7334
    sinusoidal: 3096
      harmonic: 4238
  Sorted by residual:
  dihedral pdb=" C5' ADP B1001 "
           pdb=" O5' ADP B1001 "
           pdb=" PA  ADP B1001 "
           pdb=" O2A ADP B1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  113.45 -173.45     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C5' ADP A1001 "
           pdb=" O5' ADP A1001 "
           pdb=" PA  ADP A1001 "
           pdb=" O2A ADP A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  113.42 -173.42     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" CA  SER A 671 "
           pdb=" C   SER A 671 "
           pdb=" N   THR A 672 "
           pdb=" CA  THR A 672 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.32  -29.68     0      5.00e+00 4.00e-02 3.52e+01
  ... (remaining 7331 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1622
       0.078 -    0.156: 182
       0.156 -    0.234: 7
       0.234 -    0.311: 0
       0.311 -    0.389: 1
  Chirality restraints: 1812
  Sorted by residual:
  chirality pdb=" CA  THR A 672 "
            pdb=" N   THR A 672 "
            pdb=" C   THR A 672 "
            pdb=" CB  THR A 672 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.14    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CA  GLU A 316 "
            pdb=" N   GLU A 316 "
            pdb=" C   GLU A 316 "
            pdb=" CB  GLU A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ILE B 673 "
            pdb=" N   ILE B 673 "
            pdb=" C   ILE B 673 "
            pdb=" CB  ILE B 673 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1809 not shown)

  Planarity restraints: 2060
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 670 "    0.021 2.00e-02 2.50e+03   4.26e-02 1.82e+01
        pdb=" C   LEU A 670 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   LEU A 670 "    0.028 2.00e-02 2.50e+03
        pdb=" N   SER A 671 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 670 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.49e+00
        pdb=" C   LEU B 670 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LEU B 670 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER B 671 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 671 "    0.014 2.00e-02 2.50e+03   2.76e-02 7.61e+00
        pdb=" C   SER A 671 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   SER A 671 "    0.018 2.00e-02 2.50e+03
        pdb=" N   THR A 672 "    0.016 2.00e-02 2.50e+03
  ... (remaining 2057 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 877
        2.74 -     3.28: 12622
        3.28 -     3.82: 20276
        3.82 -     4.36: 23981
        4.36 -     4.90: 38564
  Nonbonded interactions: 96320
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 469 "
            pdb=" OD1 ASP B 471 "
     model   vdw
     2.201 2.440
  nonbonded pdb=" OG1 THR A 469 "
            pdb=" OD1 ASP A 471 "
     model   vdw
     2.201 2.440
  nonbonded pdb=" OG  SER A 268 "
            pdb=" OD1 ASP A 270 "
     model   vdw
     2.280 2.440
  nonbonded pdb=" OG  SER B 268 "
            pdb=" OD1 ASP B 270 "
     model   vdw
     2.280 2.440
  nonbonded pdb=" O   VAL A 653 "
            pdb=" NH2 ARG A 685 "
     model   vdw
     2.293 2.520
  ... (remaining 96315 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          4.070
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.890
  Find NCS groups from input model:        0.560
  Set up NCS constraints:                  0.060
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
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      :  0.003   0.043  12056  Z= 0.204
  Angle     :  0.760  11.116  16286  Z= 0.383
  Chirality :  0.048   0.389   1812
  Planarity :  0.004   0.043   2060
  Dihedral  : 15.836 173.446   4582
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 17.02
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.69 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 21.35 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.23), residues: 1452
  helix:  0.50 (0.23), residues: 518
  sheet:  0.20 (0.37), residues: 212
  loop :  0.67 (0.24), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 798 
 HIS   0.004   0.001   HIS A 524 
 PHE   0.010   0.001   PHE B 571 
 TYR   0.006   0.001   TYR B 413 
 ARG   0.007   0.000   ARG A 478 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 1.490 
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  351 LEU cc_start: 0.7900 (tt) cc_final: 0.7248 (tp)
REVERT: A  456 ASP cc_start: 0.8905 (m-30) cc_final: 0.8319 (t70)
REVERT: A  692 LEU cc_start: 0.9270 (tp) cc_final: 0.9021 (tp)
REVERT: A  844 MET cc_start: 0.7277 (tmm) cc_final: 0.7032 (tmm)
REVERT: B  351 LEU cc_start: 0.7779 (tt) cc_final: 0.7215 (tp)
REVERT: B  432 TRP cc_start: 0.8378 (m-10) cc_final: 0.8029 (m-90)
REVERT: B  456 ASP cc_start: 0.8881 (m-30) cc_final: 0.8274 (t70)
REVERT: B  671 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6842 (p)
REVERT: B  672 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6154 (p)
REVERT: B  692 LEU cc_start: 0.9234 (tp) cc_final: 0.9018 (tp)
REVERT: B  844 MET cc_start: 0.7143 (tmm) cc_final: 0.6898 (tmm)
  outliers start: 19
  outliers final: 3
  residues processed: 194
  average time/residue: 0.2129
  time to fit residues: 61.9167
Evaluate side-chains
  172 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 167
  time to evaluate  : 1.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  672 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:   40.0000
   chunk 110 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 114 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 85 optimal weight:    0.5980
   chunk 132 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN
** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 668 GLN
B 309 HIS
B 349 ASN
B 668 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.0708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12056  Z= 0.155
  Angle     :  0.629  10.665  16286  Z= 0.289
  Chirality :  0.043   0.149   1812
  Planarity :  0.004   0.043   2060
  Dihedral  :  7.259 146.550   1586
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.47 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.23), residues: 1452
  helix:  0.71 (0.24), residues: 518
  sheet:  0.14 (0.38), residues: 202
  loop :  0.59 (0.24), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 432 
 HIS   0.003   0.001   HIS B 539 
 PHE   0.014   0.001   PHE A 585 
 TYR   0.012   0.001   TYR A 259 
 ARG   0.004   0.000   ARG B 478 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 171
  time to evaluate  : 1.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  456 ASP cc_start: 0.8913 (m-30) cc_final: 0.8362 (t70)
REVERT: A  671 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7185 (p)
REVERT: A  736 LEU cc_start: 0.9112 (mm) cc_final: 0.8906 (mm)
REVERT: A  844 MET cc_start: 0.7406 (tmm) cc_final: 0.7178 (tmm)
REVERT: B  313 PHE cc_start: 0.7863 (m-80) cc_final: 0.7525 (m-80)
REVERT: B  432 TRP cc_start: 0.8421 (m-10) cc_final: 0.8159 (m-90)
REVERT: B  671 SER cc_start: 0.8008 (t) cc_final: 0.7648 (p)
REVERT: B  736 LEU cc_start: 0.9007 (mm) cc_final: 0.8774 (mm)
REVERT: B  841 PHE cc_start: 0.8755 (t80) cc_final: 0.8542 (t80)
  outliers start: 39
  outliers final: 20
  residues processed: 193
  average time/residue: 0.1989
  time to fit residues: 60.4534
Evaluate side-chains
  184 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 163
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  775 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 110 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   chunk 36 optimal weight:    0.4980
   chunk 132 optimal weight:    9.9990
   chunk 143 optimal weight:    7.9990
   chunk 118 optimal weight:    6.9990
   chunk 131 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    4.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 309 HIS
A 455 ASN
** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 455 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  12056  Z= 0.351
  Angle     :  0.729   9.934  16286  Z= 0.357
  Chirality :  0.047   0.154   1812
  Planarity :  0.005   0.048   2060
  Dihedral  :  6.909 122.851   1583
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 21.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 17.78 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.23), residues: 1452
  helix:  0.82 (0.24), residues: 488
  sheet: -0.22 (0.37), residues: 198
  loop :  0.45 (0.24), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 432 
 HIS   0.007   0.002   HIS B 309 
 PHE   0.020   0.002   PHE A 530 
 TYR   0.018   0.002   TYR A 212 
 ARG   0.005   0.001   ARG A 167 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 168
  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: A  429 ILE cc_start: 0.9220 (pp) cc_final: 0.9011 (pp)
REVERT: A  522 CYS cc_start: 0.7530 (p) cc_final: 0.7272 (p)
REVERT: B  313 PHE cc_start: 0.8066 (m-80) cc_final: 0.7719 (m-80)
REVERT: B  351 LEU cc_start: 0.7591 (tt) cc_final: 0.7013 (tp)
REVERT: B  407 LEU cc_start: 0.9577 (tp) cc_final: 0.9354 (tp)
REVERT: B  522 CYS cc_start: 0.7475 (p) cc_final: 0.7205 (p)
REVERT: B  671 SER cc_start: 0.8283 (t) cc_final: 0.8080 (p)
  outliers start: 48
  outliers final: 35
  residues processed: 190
  average time/residue: 0.1997
  time to fit residues: 57.9603
Evaluate side-chains
  193 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 158
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  584 GLU
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  751 LEU
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  875 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 131 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 68 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   chunk 133 optimal weight:    1.9990
   chunk 141 optimal weight:   20.0000
   chunk 69 optimal weight:    4.9990
   chunk 126 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 539 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  12056  Z= 0.355
  Angle     :  0.720  10.078  16286  Z= 0.351
  Chirality :  0.047   0.228   1812
  Planarity :  0.005   0.047   2060
  Dihedral  :  6.743 108.396   1582
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 21.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 19.15 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.23), residues: 1452
  helix:  0.64 (0.23), residues: 490
  sheet: -0.60 (0.36), residues: 198
  loop :  0.25 (0.24), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.002   TRP A 432 
 HIS   0.008   0.002   HIS A 309 
 PHE   0.019   0.002   PHE A 530 
 TYR   0.013   0.002   TYR B 413 
 ARG   0.004   0.001   ARG B 430 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 167
  time to evaluate  : 1.362 
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  407 LEU cc_start: 0.9582 (tp) cc_final: 0.9265 (tp)
REVERT: A  429 ILE cc_start: 0.9243 (pp) cc_final: 0.9033 (pp)
REVERT: A  432 TRP cc_start: 0.8271 (m-90) cc_final: 0.8023 (m-90)
REVERT: A  522 CYS cc_start: 0.7612 (p) cc_final: 0.7300 (p)
REVERT: B  313 PHE cc_start: 0.8183 (m-80) cc_final: 0.7760 (m-80)
REVERT: B  522 CYS cc_start: 0.7645 (p) cc_final: 0.7362 (p)
  outliers start: 56
  outliers final: 41
  residues processed: 196
  average time/residue: 0.1964
  time to fit residues: 59.3948
Evaluate side-chains
  200 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 159
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  393 ASN
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  584 GLU
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  393 ASN
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  875 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 117 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 2 optimal weight:    8.9990
   chunk 105 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 120 optimal weight:    0.0000
   chunk 97 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 126 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    2.1190

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 668 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12056  Z= 0.221
  Angle     :  0.679  10.836  16286  Z= 0.315
  Chirality :  0.045   0.312   1812
  Planarity :  0.004   0.054   2060
  Dihedral  :  6.261  91.806   1582
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 18.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.82 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.23), residues: 1452
  helix:  0.80 (0.24), residues: 478
  sheet: -0.40 (0.37), residues: 182
  loop :  0.18 (0.24), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 432 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.019   0.002   PHE B 571 
 TYR   0.009   0.001   TYR B 413 
 ARG   0.004   0.000   ARG A 402 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 176
  time to evaluate  : 1.368 
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  403 LEU cc_start: 0.8415 (tp) cc_final: 0.7970 (tp)
REVERT: B  522 CYS cc_start: 0.7583 (p) cc_final: 0.7310 (p)
REVERT: B  740 TYR cc_start: 0.8881 (p90) cc_final: 0.8649 (p90)
  outliers start: 40
  outliers final: 29
  residues processed: 197
  average time/residue: 0.2061
  time to fit residues: 61.3100
Evaluate side-chains
  199 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 170
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  393 ASN
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  584 GLU
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  393 ASN
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  677 SER
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  875 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 127 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 141 optimal weight:    0.7980
   chunk 117 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  12056  Z= 0.170
  Angle     :  0.694  13.150  16286  Z= 0.310
  Chirality :  0.045   0.322   1812
  Planarity :  0.004   0.056   2060
  Dihedral  :  5.924  81.815   1582
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 21.66 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.23), residues: 1452
  helix:  0.80 (0.25), residues: 480
  sheet: -0.13 (0.36), residues: 190
  loop :  0.28 (0.24), residues: 782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 432 
 HIS   0.005   0.001   HIS A 524 
 PHE   0.018   0.001   PHE A 571 
 TYR   0.008   0.001   TYR A 740 
 ARG   0.005   0.000   ARG A 488 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 1.455 
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  351 LEU cc_start: 0.7313 (tp) cc_final: 0.7112 (tt)
REVERT: B  323 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8645 (pp)
REVERT: B  351 LEU cc_start: 0.7285 (tt) cc_final: 0.6910 (tt)
REVERT: B  403 LEU cc_start: 0.8202 (mm) cc_final: 0.7999 (mp)
REVERT: B  740 TYR cc_start: 0.8862 (p90) cc_final: 0.8618 (p90)
  outliers start: 31
  outliers final: 20
  residues processed: 195
  average time/residue: 0.2027
  time to fit residues: 60.4765
Evaluate side-chains
  190 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  393 ASN
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  775 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 136 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9980
   chunk 79 optimal weight:    0.3980
   chunk 118 optimal weight:    0.0060
   chunk 78 optimal weight:    2.9990
   chunk 140 optimal weight:   20.0000
   chunk 88 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   overall best weight:    1.2800

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12056  Z= 0.179
  Angle     :  0.699  15.305  16286  Z= 0.315
  Chirality :  0.045   0.291   1812
  Planarity :  0.004   0.056   2060
  Dihedral  :  5.785  76.417   1582
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.26 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.23), residues: 1452
  helix:  0.80 (0.24), residues: 480
  sheet: -0.08 (0.36), residues: 190
  loop :  0.26 (0.24), residues: 782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.002   TRP A 432 
 HIS   0.004   0.001   HIS A 524 
 PHE   0.027   0.001   PHE B 841 
 TYR   0.007   0.001   TYR A 740 
 ARG   0.004   0.000   ARG B 430 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 179
  time to evaluate  : 1.513 
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  403 LEU cc_start: 0.8500 (tp) cc_final: 0.8251 (tt)
REVERT: A  410 CYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9052 (p)
REVERT: B  403 LEU cc_start: 0.8178 (mm) cc_final: 0.7974 (mp)
REVERT: B  740 TYR cc_start: 0.8846 (p90) cc_final: 0.8599 (p90)
  outliers start: 36
  outliers final: 27
  residues processed: 200
  average time/residue: 0.1952
  time to fit residues: 60.8987
Evaluate side-chains
  198 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 170
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  393 ASN
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  393 ASN
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  677 SER
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  875 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 89 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 110 optimal weight:    2.9990
   chunk 128 optimal weight:    5.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 455 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12056  Z= 0.189
  Angle     :  0.713  15.416  16286  Z= 0.320
  Chirality :  0.046   0.322   1812
  Planarity :  0.004   0.056   2060
  Dihedral  :  5.727  70.452   1582
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 22.26 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.23), residues: 1452
  helix:  0.82 (0.25), residues: 480
  sheet: -0.17 (0.36), residues: 190
  loop :  0.25 (0.24), residues: 782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.110   0.002   TRP A 432 
 HIS   0.004   0.001   HIS A 524 
 PHE   0.013   0.001   PHE A 571 
 TYR   0.007   0.001   TYR A 740 
 ARG   0.004   0.000   ARG B 430 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 1.404 
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  351 LEU cc_start: 0.7754 (tt) cc_final: 0.7168 (tp)
REVERT: A  403 LEU cc_start: 0.8622 (tp) cc_final: 0.8376 (tt)
REVERT: A  410 CYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9030 (p)
REVERT: B  323 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8667 (pp)
REVERT: B  403 LEU cc_start: 0.8227 (mm) cc_final: 0.7979 (mp)
REVERT: B  740 TYR cc_start: 0.8839 (p90) cc_final: 0.8599 (p90)
REVERT: B  767 MET cc_start: 0.7720 (tpp) cc_final: 0.7423 (tpp)
  outliers start: 35
  outliers final: 30
  residues processed: 185
  average time/residue: 0.2009
  time to fit residues: 57.0695
Evaluate side-chains
  196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  393 ASN
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  393 ASN
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  677 SER
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  874 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 134 optimal weight:    8.9990
   chunk 122 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 102 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 118 optimal weight:    6.9990
   chunk 124 optimal weight:    6.9990
   chunk 130 optimal weight:    8.9990
   chunk 86 optimal weight:    9.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS
A 778 ASN
B 769 HIS
B 778 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12056  Z= 0.310
  Angle     :  0.768  15.216  16286  Z= 0.360
  Chirality :  0.048   0.366   1812
  Planarity :  0.005   0.054   2060
  Dihedral  :  6.030  69.901   1582
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 22.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 22.26 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.23), residues: 1452
  helix:  0.68 (0.24), residues: 500
  sheet: -0.44 (0.36), residues: 190
  loop :  0.21 (0.25), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.135   0.003   TRP A 432 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.016   0.002   PHE A 841 
 TYR   0.016   0.002   TYR B 259 
 ARG   0.003   0.000   ARG B 430 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 172
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.7623 (tt) cc_final: 0.7025 (tp)
REVERT: A  403 LEU cc_start: 0.8704 (tp) cc_final: 0.8340 (tt)
REVERT: A  410 CYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9175 (p)
REVERT: B  323 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8704 (pp)
REVERT: B  403 LEU cc_start: 0.8262 (mm) cc_final: 0.8003 (mp)
REVERT: B  522 CYS cc_start: 0.7677 (p) cc_final: 0.7315 (p)
REVERT: B  572 ASP cc_start: 0.8313 (t0) cc_final: 0.8082 (t0)
  outliers start: 45
  outliers final: 37
  residues processed: 193
  average time/residue: 0.1976
  time to fit residues: 58.7782
Evaluate side-chains
  202 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 163
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  393 ASN
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  393 ASN
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  677 SER
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  874 ASN
Chi-restraints excluded: chain B residue  875 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 138 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 96 optimal weight:    0.0670
   chunk 145 optimal weight:    6.9990
   chunk 133 optimal weight:    5.9990
   chunk 115 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 89 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 92 optimal weight:    6.9990
   overall best weight:    1.0920

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12056  Z= 0.180
  Angle     :  0.738  16.218  16286  Z= 0.332
  Chirality :  0.046   0.401   1812
  Planarity :  0.004   0.056   2060
  Dihedral  :  5.676  58.352   1580
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 23.56 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.23), residues: 1452
  helix:  0.73 (0.24), residues: 482
  sheet: -0.38 (0.36), residues: 190
  loop :  0.24 (0.24), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.134   0.002   TRP A 432 
 HIS   0.010   0.001   HIS A 539 
 PHE   0.013   0.001   PHE A 571 
 TYR   0.016   0.001   TYR B 259 
 ARG   0.003   0.000   ARG A 488 

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

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

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2904 Ramachandran restraints generated.
    1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 178
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.7548 (tt) cc_final: 0.6985 (tp)
REVERT: A  403 LEU cc_start: 0.8774 (tp) cc_final: 0.8446 (tt)
REVERT: B  323 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8713 (pp)
REVERT: B  403 LEU cc_start: 0.8177 (mm) cc_final: 0.7948 (mp)
  outliers start: 29
  outliers final: 26
  residues processed: 193
  average time/residue: 0.2103
  time to fit residues: 61.5637
Evaluate side-chains
  196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  393 ASN
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  553 MET
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 THR
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  778 ASN
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  874 ASN
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  393 ASN
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  677 SER
Chi-restraints excluded: chain B residue  686 THR
Chi-restraints excluded: chain B residue  692 LEU
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  874 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 116 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9990
   chunk 119 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 101 optimal weight:    0.4980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 309 HIS
** A 640 HIS ** 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 = 0.4022 r_free = 0.4022 target = 0.104428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.075941 restraints weight = 34796.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.078954 restraints weight = 19067.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.080985 restraints weight = 13068.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12056  Z= 0.171
  Angle     :  0.736  16.794  16286  Z= 0.328
  Chirality :  0.046   0.403   1812
  Planarity :  0.004   0.055   2060
  Dihedral  :  5.559  57.276   1580
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 17.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 23.33 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.23), residues: 1452
  helix:  0.77 (0.24), residues: 480
  sheet: -0.34 (0.35), residues: 212
  loop :  0.28 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.133   0.002   TRP A 432 
 HIS   0.008   0.001   HIS A 539 
 PHE   0.020   0.001   PHE A 841 
 TYR   0.014   0.001   TYR B 259 
 ARG   0.004   0.000   ARG A 488 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2334.45 seconds
wall clock time: 43 minutes 55.68 seconds (2635.68 seconds total)