Starting phenix.real_space_refine (version: 1.21rc1)
on Sat Apr 22 05:05:29 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/04_2023/5oyg_3861.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/04_2023/5oyg_3861.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/04_2023/5oyg_3861.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/04_2023/5oyg_3861.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/04_2023/5oyg_3861.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/04_2023/5oyg_3861.pdb"
  }
  resolution = 4.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    7566      2.51       5
     N    1906      2.21       5
     O    2052      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  127": "NH1" <-> "NH2"
    Residue "A ARG  298": "NH1" <-> "NH2"
    Residue "A ARG  429": "NH1" <-> "NH2"
    Residue "A ARG  535": "NH1" <-> "NH2"
    Residue "A TYR  687": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  747": "NH1" <-> "NH2"
    Residue "B ARG  127": "NH1" <-> "NH2"
    Residue "B ARG  298": "NH1" <-> "NH2"
    Residue "B ARG  429": "NH1" <-> "NH2"
    Residue "B ARG  535": "NH1" <-> "NH2"
    Residue "B TYR  687": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  747": "NH1" <-> "NH2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 11596
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 709, 5798
          Classifications: {'peptide': 709}
          Link IDs: {'PTRANS': 31, 'TRANS': 677}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 5798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 709, 5798
          Classifications: {'peptide': 709}
          Link IDs: {'PTRANS': 31, 'TRANS': 677}
          Chain breaks: 4
  Time building chain proxies: 6.24, per 1000 atoms: 0.54
  Number of scatterers: 11596
  At special positions: 0
  Unit cell: (85.995, 124.215, 121.485, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    2052      8.00
     N    1906      7.00
     C    7566      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 386 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 625 " - pdb=" SG  CYS A 630 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 386 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 625 " - pdb=" SG  CYS B 630 " distance=2.04

  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: 4.61
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2716

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      62.6% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
      removed outlier: 3.790A  pdb=" N   LEU A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 181
      removed outlier: 3.590A  pdb=" N   THR A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 205 through 211
    Processing helix  chain 'A' and resid 242 through 257
      removed outlier: 3.596A  pdb=" N   THR A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 275
      removed outlier: 3.704A  pdb=" N   GLY A 275 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 316 through 325
    Processing helix  chain 'A' and resid 325 through 359
      removed outlier: 3.643A  pdb=" N   GLY A 329 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ILE A 343 " --> pdb=" O   THR A 339 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
      removed outlier: 3.638A  pdb=" N   THR A 359 " --> pdb=" O   TYR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 363
      removed outlier: 3.767A  pdb=" N   ASN A 363 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 360 through 363'
    Processing helix  chain 'A' and resid 364 through 371
    Processing helix  chain 'A' and resid 395 through 405
    Processing helix  chain 'A' and resid 408 through 438
    Processing helix  chain 'A' and resid 452 through 466
      removed outlier: 3.833A  pdb=" N   ALA A 456 " --> pdb=" O   ASP A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 519
    Processing helix  chain 'A' and resid 523 through 527
      removed outlier: 4.420A  pdb=" N   SER A 526 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER A 527 " --> pdb=" O   MET A 524 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 523 through 527'
    Processing helix  chain 'A' and resid 536 through 569
      removed outlier: 3.538A  pdb=" N   ALA A 540 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   GLU A 555 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   VAL A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 569 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 601
      removed outlier: 3.816A  pdb=" N   LEU A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      Proline residue:  A 595  - end of helix
    Processing helix  chain 'A' and resid 630 through 656
      removed outlier: 3.952A  pdb=" N   LEU A 634 " --> pdb=" O   CYS A 630 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE A 640 " --> pdb=" O   ILE A 636 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 641 " --> pdb=" O   GLN A 637 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   GLN A 646 " --> pdb=" O   MET A 642 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   LEU A 647 " --> pdb=" O   LEU A 643 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   GLU A 654 " --> pdb=" O   ASN A 650 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ILE A 655 " --> pdb=" O   ASN A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 692
      removed outlier: 4.062A  pdb=" N   ASN A 692 " --> pdb=" O   GLU A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 715
      removed outlier: 4.249A  pdb=" N   GLU A 705 " --> pdb=" O   PRO A 701 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   MET A 706 " --> pdb=" O   GLU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 744
      removed outlier: 3.586A  pdb=" N   PHE A 726 " --> pdb=" O   LEU A 722 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ILE A 733 " --> pdb=" O   LEU A 729 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG A 736 " --> pdb=" O   ILE A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 781
      removed outlier: 4.009A  pdb=" N   ASN A 762 " --> pdb=" O   GLY A 758 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   VAL A 772 " --> pdb=" O   GLY A 768 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   ILE A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A 774 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 795
      removed outlier: 3.549A  pdb=" N   LEU A 789 " --> pdb=" O   PHE A 785 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR A 795 " --> pdb=" O   TYR A 791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 809
    Processing helix  chain 'A' and resid 854 through 886
      removed outlier: 4.038A  pdb=" N   TRP A 858 " --> pdb=" O   SER A 854 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASP A 883 " --> pdb=" O   SER A 879 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE A 886 " --> pdb=" O   VAL A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 909
      removed outlier: 3.510A  pdb=" N   SER A 894 " --> pdb=" O   PRO A 890 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 174
      removed outlier: 3.791A  pdb=" N   LEU B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 181
      removed outlier: 3.590A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 204
      No H-bonds generated for 'chain 'B' and resid 202 through 204'
    Processing helix  chain 'B' and resid 205 through 211
    Processing helix  chain 'B' and resid 242 through 257
      removed outlier: 3.597A  pdb=" N   THR B 257 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 275
      removed outlier: 3.703A  pdb=" N   GLY B 275 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 305
    Processing helix  chain 'B' and resid 316 through 325
    Processing helix  chain 'B' and resid 325 through 359
      removed outlier: 3.644A  pdb=" N   GLY B 329 " --> pdb=" O   GLY B 325 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ILE B 343 " --> pdb=" O   THR B 339 " (cutoff:3.500A)
      Proline residue:  B 344  - end of helix
      removed outlier: 3.638A  pdb=" N   THR B 359 " --> pdb=" O   TYR B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 363
      removed outlier: 3.766A  pdb=" N   ASN B 363 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 360 through 363'
    Processing helix  chain 'B' and resid 364 through 371
    Processing helix  chain 'B' and resid 395 through 405
    Processing helix  chain 'B' and resid 408 through 438
    Processing helix  chain 'B' and resid 452 through 466
      removed outlier: 3.833A  pdb=" N   ALA B 456 " --> pdb=" O   ASP B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 490 through 519
    Processing helix  chain 'B' and resid 523 through 527
      removed outlier: 4.421A  pdb=" N   SER B 526 " --> pdb=" O   ALA B 523 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER B 527 " --> pdb=" O   MET B 524 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 523 through 527'
    Processing helix  chain 'B' and resid 536 through 569
      removed outlier: 3.538A  pdb=" N   ALA B 540 " --> pdb=" O   VAL B 536 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   GLU B 555 " --> pdb=" O   ILE B 551 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   VAL B 556 " --> pdb=" O   LEU B 552 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL B 569 " --> pdb=" O   THR B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 601
      removed outlier: 3.815A  pdb=" N   LEU B 587 " --> pdb=" O   LYS B 583 " (cutoff:3.500A)
      Proline residue:  B 595  - end of helix
    Processing helix  chain 'B' and resid 630 through 656
      removed outlier: 3.951A  pdb=" N   LEU B 634 " --> pdb=" O   CYS B 630 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE B 640 " --> pdb=" O   ILE B 636 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 641 " --> pdb=" O   GLN B 637 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   GLN B 646 " --> pdb=" O   MET B 642 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   LEU B 647 " --> pdb=" O   LEU B 643 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLU B 654 " --> pdb=" O   ASN B 650 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ILE B 655 " --> pdb=" O   ASN B 651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 685 through 692
      removed outlier: 4.064A  pdb=" N   ASN B 692 " --> pdb=" O   GLU B 688 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 699 through 715
      removed outlier: 4.254A  pdb=" N   GLU B 705 " --> pdb=" O   PRO B 701 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   MET B 706 " --> pdb=" O   GLU B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 722 through 744
      removed outlier: 3.587A  pdb=" N   PHE B 726 " --> pdb=" O   LEU B 722 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ILE B 733 " --> pdb=" O   LEU B 729 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG B 736 " --> pdb=" O   ILE B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 781
      removed outlier: 4.008A  pdb=" N   ASN B 762 " --> pdb=" O   GLY B 758 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   VAL B 772 " --> pdb=" O   GLY B 768 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   ILE B 773 " --> pdb=" O   LYS B 769 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE B 774 " --> pdb=" O   LEU B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 795
      removed outlier: 3.549A  pdb=" N   LEU B 789 " --> pdb=" O   PHE B 785 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR B 795 " --> pdb=" O   TYR B 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 809
    Processing helix  chain 'B' and resid 854 through 886
      removed outlier: 4.036A  pdb=" N   TRP B 858 " --> pdb=" O   SER B 854 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP B 883 " --> pdb=" O   SER B 879 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE B 886 " --> pdb=" O   VAL B 882 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 909
      removed outlier: 3.510A  pdb=" N   SER B 894 " --> pdb=" O   PRO B 890 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189
      removed outlier: 4.024A  pdb=" N   SER A 196 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASP A 123 " --> pdb=" O   GLN A 199 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   PHE A 126 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218
    Processing sheet with id=AA3, first strand: chain 'A' and resid 615 through 616
      removed outlier: 3.658A  pdb=" N   PHE A 620 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 812 through 813
    Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 189
      removed outlier: 4.022A  pdb=" N   SER B 196 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASP B 123 " --> pdb=" O   GLN B 199 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   PHE B 126 " --> pdb=" O   SER B 278 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 217 through 218
    Processing sheet with id=AA7, first strand: chain 'B' and resid 615 through 616
      removed outlier: 3.659A  pdb=" N   PHE B 620 " --> pdb=" O   ILE B 616 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 812 through 813

    616 hydrogen bonds defined for protein.
    1830 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: 3.22

  Time building geometry restraints manager: 4.87 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3393
        1.33 -     1.46: 2108
        1.46 -     1.58: 6271
        1.58 -     1.70: 0
        1.70 -     1.82: 118
  Bond restraints: 11890
  Sorted by residual:
  bond pdb=" CA  ASP B 203 "
       pdb=" C   ASP B 203 "
    ideal  model  delta    sigma   weight residual
    1.521  1.548 -0.027 1.11e-02 8.12e+03 5.71e+00
  bond pdb=" C   MET A 176 "
       pdb=" N   PRO A 177 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.028 1.19e-02 7.06e+03 5.52e+00
  bond pdb=" CA  ILE B 657 "
       pdb=" C   ILE B 657 "
    ideal  model  delta    sigma   weight residual
    1.524  1.549 -0.024 1.05e-02 9.07e+03 5.42e+00
  bond pdb=" C   MET B 176 "
       pdb=" N   PRO B 177 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.028 1.19e-02 7.06e+03 5.42e+00
  bond pdb=" CA  ASP A 203 "
       pdb=" C   ASP A 203 "
    ideal  model  delta    sigma   weight residual
    1.521  1.547 -0.026 1.11e-02 8.12e+03 5.35e+00
  ... (remaining 11885 not shown)

  Histogram of bond angle deviations from ideal:
       97.74 -   105.03: 246
      105.03 -   112.31: 5010
      112.31 -   119.59: 4684
      119.59 -   126.88: 6027
      126.88 -   134.16: 127
  Bond angle restraints: 16094
  Sorted by residual:
  angle pdb=" C   HIS B 453 "
        pdb=" N   PRO B 454 "
        pdb=" CA  PRO B 454 "
      ideal   model   delta    sigma   weight residual
     119.87  114.38    5.49 1.04e+00 9.25e-01 2.79e+01
  angle pdb=" C   HIS A 453 "
        pdb=" N   PRO A 454 "
        pdb=" CA  PRO A 454 "
      ideal   model   delta    sigma   weight residual
     119.87  114.45    5.42 1.04e+00 9.25e-01 2.71e+01
  angle pdb=" C   ILE B 657 "
        pdb=" N   PRO B 658 "
        pdb=" CA  PRO B 658 "
      ideal   model   delta    sigma   weight residual
     119.05  124.73   -5.68 1.11e+00 8.12e-01 2.62e+01
  angle pdb=" C   ILE A 657 "
        pdb=" N   PRO A 658 "
        pdb=" CA  PRO A 658 "
      ideal   model   delta    sigma   weight residual
     119.05  124.68   -5.63 1.11e+00 8.12e-01 2.57e+01
  angle pdb=" N   SER A 811 "
        pdb=" CA  SER A 811 "
        pdb=" C   SER A 811 "
      ideal   model   delta    sigma   weight residual
     110.91  116.32   -5.41 1.17e+00 7.31e-01 2.14e+01
  ... (remaining 16089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 6441
       16.26 -    32.52: 521
       32.52 -    48.79: 122
       48.79 -    65.05: 10
       65.05 -    81.31: 12
  Dihedral angle restraints: 7106
    sinusoidal: 2910
      harmonic: 4196
  Sorted by residual:
  dihedral pdb=" CB  CYS B 382 "
           pdb=" SG  CYS B 382 "
           pdb=" SG  CYS B 386 "
           pdb=" CB  CYS B 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.58  -68.42     1      1.00e+01 1.00e-02 6.07e+01
  dihedral pdb=" CB  CYS A 382 "
           pdb=" SG  CYS A 382 "
           pdb=" SG  CYS A 386 "
           pdb=" CB  CYS A 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.75  -68.25     1      1.00e+01 1.00e-02 6.04e+01
  dihedral pdb=" CB  CYS B 625 "
           pdb=" SG  CYS B 625 "
           pdb=" SG  CYS B 630 "
           pdb=" CB  CYS B 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.34  -66.34     1      1.00e+01 1.00e-02 5.75e+01
  ... (remaining 7103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 1249
       0.100 -    0.200: 442
       0.200 -    0.299: 59
       0.299 -    0.399: 17
       0.399 -    0.499: 7
  Chirality restraints: 1774
  Sorted by residual:
  chirality pdb=" CA  PHE A 505 "
            pdb=" N   PHE A 505 "
            pdb=" C   PHE A 505 "
            pdb=" CB  PHE A 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.22e+00
  chirality pdb=" CA  PHE B 505 "
            pdb=" N   PHE B 505 "
            pdb=" C   PHE B 505 "
            pdb=" CB  PHE B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.17e+00
  chirality pdb=" CA  THR A 594 "
            pdb=" N   THR A 594 "
            pdb=" C   THR A 594 "
            pdb=" CB  THR A 594 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.07    0.46 2.00e-01 2.50e+01 5.20e+00
  ... (remaining 1771 not shown)

  Planarity restraints: 2020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 406 "   -0.048 5.00e-02 4.00e+02   7.36e-02 8.68e+00
        pdb=" N   PRO A 407 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 407 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 407 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 406 "    0.048 5.00e-02 4.00e+02   7.36e-02 8.66e+00
        pdb=" N   PRO B 407 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 407 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 407 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 222 "   -0.043 5.00e-02 4.00e+02   6.53e-02 6.82e+00
        pdb=" N   PRO B 223 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 223 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 223 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2017 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2743
        2.81 -     3.33: 11084
        3.33 -     3.85: 18028
        3.85 -     4.38: 19669
        4.38 -     4.90: 33725
  Nonbonded interactions: 85249
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 791 "
            pdb=" O   HIS B 802 "
     model   vdw
     2.282 2.440
  nonbonded pdb=" OH  TYR A 791 "
            pdb=" O   HIS A 802 "
     model   vdw
     2.283 2.440
  nonbonded pdb=" NH2 ARG A 515 "
            pdb=" O   MET A 622 "
     model   vdw
     2.334 2.520
  nonbonded pdb=" NH2 ARG B 515 "
            pdb=" O   MET B 622 "
     model   vdw
     2.334 2.520
  nonbonded pdb=" O   ALA A 600 "
            pdb=" OG1 THR A 782 "
     model   vdw
     2.336 2.440
  ... (remaining 85244 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:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          4.830
  Check model and map are aligned:         0.180
  Set scattering table:                    0.110
  Process input model:                     31.050
  Find NCS groups from input model:        0.610
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
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      :  0.007   0.037  11890  Z= 0.469
  Angle     :  1.269   9.151  16094  Z= 0.800
  Chirality :  0.103   0.499   1774
  Planarity :  0.007   0.074   2020
  Dihedral  : 12.530  81.310   4366
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer Outliers :  1.98 %
  Cbeta Deviations :  0.74 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.19), residues: 1398
  helix: -1.60 (0.15), residues: 790
  sheet: -1.66 (0.98), residues: 22
  loop : -3.11 (0.24), residues: 586

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 268
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 25
  outliers final: 0
  residues processed: 285
  average time/residue: 0.2932
  time to fit residues: 110.6264
Evaluate side-chains
  163 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.354 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.8005
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 127 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 206 GLN
A 646 GLN
A 709 GLN
** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 206 GLN
B 646 GLN
B 709 GLN
** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11890  Z= 0.188
  Angle     :  0.663  11.174  16094  Z= 0.338
  Chirality :  0.043   0.178   1774
  Planarity :  0.005   0.056   2020
  Dihedral  :  5.103  22.674   1562
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer Outliers :  0.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.22), residues: 1398
  helix:  0.52 (0.17), residues: 838
  sheet: -1.23 (0.89), residues: 28
  loop : -2.89 (0.26), residues: 532

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 210
  time to evaluate  : 1.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2366
  time to fit residues: 71.9508
Evaluate side-chains
  142 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.396 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.9645
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:    0.0570
   chunk 105 optimal weight:    7.9990
   chunk 86 optimal weight:    0.7980
   chunk 35 optimal weight:   20.0000
   chunk 127 optimal weight:    3.9990
   chunk 137 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 126 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 102 optimal weight:   10.0000
   overall best weight:    1.3300

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

Flipped N/Q/H residues before XYZ refinement:
A 206 GLN
** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 818 GLN
B 206 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11890  Z= 0.195
  Angle     :  0.635   9.624  16094  Z= 0.327
  Chirality :  0.042   0.182   1774
  Planarity :  0.004   0.053   2020
  Dihedral  :  4.817  21.090   1562
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer Outliers :  0.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.23), residues: 1398
  helix:  1.22 (0.18), residues: 842
  sheet: -1.94 (0.76), residues: 48
  loop : -2.83 (0.27), residues: 508

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 1.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2500
  time to fit residues: 64.5166
Evaluate side-chains
  130 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.457 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.9708
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 125 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 127 optimal weight:    2.9990
   chunk 135 optimal weight:    5.9990
   chunk 121 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 818 GLN
B 206 GLN
B 818 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11890  Z= 0.207
  Angle     :  0.626   9.195  16094  Z= 0.323
  Chirality :  0.043   0.204   1774
  Planarity :  0.004   0.046   2020
  Dihedral  :  4.707  20.438   1562
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer Outliers :  0.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.23), residues: 1398
  helix:  1.51 (0.18), residues: 842
  sheet: -1.89 (0.78), residues: 48
  loop : -2.75 (0.27), residues: 508

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 1.581 
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
  outliers start: 1
  outliers final: 0
  residues processed: 174
  average time/residue: 0.2522
  time to fit residues: 63.2964
Evaluate side-chains
  126 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.574 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.1253
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 55 optimal weight:    0.3980
   chunk 115 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 121 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0270
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
B 206 GLN
B 818 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.055  11890  Z= 0.160
  Angle     :  0.604   8.887  16094  Z= 0.306
  Chirality :  0.042   0.182   1774
  Planarity :  0.004   0.044   2020
  Dihedral  :  4.511  19.931   1562
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer Outliers :  0.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.24), residues: 1398
  helix:  1.75 (0.18), residues: 832
  sheet: -1.78 (0.81), residues: 48
  loop : -2.68 (0.27), residues: 518

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 179
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2482
  time to fit residues: 65.3743
Evaluate side-chains
  135 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.525 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.0239
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 121 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 135 optimal weight:    0.2980
   chunk 112 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 44 optimal weight:    0.1980
   chunk 71 optimal weight:    2.9990
   chunk 130 optimal weight:    7.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 206 GLN
B 206 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11890  Z= 0.155
  Angle     :  0.619   8.699  16094  Z= 0.310
  Chirality :  0.042   0.174   1774
  Planarity :  0.004   0.045   2020
  Dihedral  :  4.366  19.472   1562
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.24), residues: 1398
  helix:  1.78 (0.18), residues: 838
  sheet: -1.54 (0.82), residues: 48
  loop : -2.66 (0.27), residues: 512

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2298
  time to fit residues: 61.3715
Evaluate side-chains
  137 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.479 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.0065
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 114 optimal weight:    8.9990
   chunk 75 optimal weight:    0.5980
   chunk 134 optimal weight:    0.0060
   chunk 84 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0770
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.3358

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

Flipped N/Q/H residues before XYZ refinement:
** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 206 GLN
** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.4455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.063  11890  Z= 0.200
  Angle     :  0.634   8.927  16094  Z= 0.322
  Chirality :  0.043   0.172   1774
  Planarity :  0.004   0.043   2020
  Dihedral  :  4.374  18.732   1562
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.24), residues: 1398
  helix:  1.93 (0.18), residues: 838
  sheet: -1.54 (0.80), residues: 48
  loop : -2.61 (0.27), residues: 512

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.2418
  time to fit residues: 61.4849
Evaluate side-chains
  129 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.405 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.8584
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0020
   chunk 66 optimal weight:    0.6980
   chunk 12 optimal weight:    7.9990
   chunk 106 optimal weight:    0.8980
   chunk 122 optimal weight:    0.5980
   chunk 129 optimal weight:    7.9990
   overall best weight:    1.0390

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

Flipped N/Q/H residues before XYZ refinement:
** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11890  Z= 0.182
  Angle     :  0.653   8.926  16094  Z= 0.327
  Chirality :  0.043   0.211   1774
  Planarity :  0.004   0.044   2020
  Dihedral  :  4.380  19.070   1562
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.23), residues: 1398
  helix:  1.90 (0.18), residues: 832
  sheet: -1.58 (0.80), residues: 48
  loop : -2.51 (0.27), residues: 518

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2316
  time to fit residues: 57.9493
Evaluate side-chains
  124 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.422 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.9079
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 125 optimal weight:    0.0870
   chunk 129 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 98 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 118 optimal weight:    8.9990
   chunk 82 optimal weight:    3.9990
   chunk 132 optimal weight:    0.4980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.4820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11890  Z= 0.166
  Angle     :  0.651   9.051  16094  Z= 0.324
  Chirality :  0.042   0.190   1774
  Planarity :  0.004   0.043   2020
  Dihedral  :  4.378  19.434   1562
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.24), residues: 1398
  helix:  1.97 (0.18), residues: 832
  sheet: -1.51 (0.82), residues: 48
  loop : -2.40 (0.27), residues: 518

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2357
  time to fit residues: 62.3720
Evaluate side-chains
  140 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.510 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.9900
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 139 optimal weight:    0.7980
   chunk 128 optimal weight:    0.9990
   chunk 111 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 85 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 88 optimal weight:    0.5980
   chunk 118 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.4946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11890  Z= 0.171
  Angle     :  0.656   8.585  16094  Z= 0.326
  Chirality :  0.043   0.207   1774
  Planarity :  0.004   0.043   2020
  Dihedral  :  4.305  21.654   1562
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.24), residues: 1398
  helix:  1.93 (0.18), residues: 838
  sheet: -1.35 (0.83), residues: 48
  loop : -2.38 (0.28), residues: 512

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

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

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2796 Ramachandran restraints generated.
    1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2209
  time to fit residues: 56.8043
Evaluate side-chains
  135 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.504 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.0688
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 102 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 111 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 114 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0970
   chunk 97 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.076691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.059368 restraints weight = 44698.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.060934 restraints weight = 25094.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.061945 restraints weight = 17401.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.4939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11890  Z= 0.240
  Angle     :  0.683   9.151  16094  Z= 0.343
  Chirality :  0.044   0.197   1774
  Planarity :  0.004   0.042   2020
  Dihedral  :  4.451  21.453   1562
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.24), residues: 1398
  helix:  1.98 (0.18), residues: 832
  sheet: -1.56 (0.77), residues: 48
  loop : -2.27 (0.28), residues: 518

===============================================================================
Job complete
usr+sys time: 2163.74 seconds
wall clock time: 40 minutes 25.80 seconds (2425.80 seconds total)