Starting phenix.real_space_refine
on Tue Jan 14 08:14:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bco_44432/01_2025/9bco_44432.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bco_44432/01_2025/9bco_44432.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bco_44432/01_2025/9bco_44432.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bco_44432/01_2025/9bco_44432.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bco_44432/01_2025/9bco_44432.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bco_44432/01_2025/9bco_44432.cif"
  }
  resolution = 4.4
  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=   0.002 sd=   0.046
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S       9      5.16       5
     C    3782      2.51       5
     N    1170      2.21       5
     O    1197      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6164
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 521, 3054
          Classifications: {'peptide': 521}
          Incomplete info: {'truncation_to_alanine': 328}
          Link IDs: {'PTRANS': 21, 'TRANS': 499}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 1142
          Unresolved non-hydrogen angles: 1450
          Unresolved non-hydrogen dihedrals: 906
          Unresolved non-hydrogen chiralities: 126
          Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 10, 'GLU:plan': 38, 'ARG:plan': 31}
          Unresolved non-hydrogen planarities: 619
    Chain: "B"
      Number of atoms: 3048
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 517, 3048
          Classifications: {'peptide': 517}
          Incomplete info: {'truncation_to_alanine': 316}
          Link IDs: {'PTRANS': 21, 'TRANS': 495}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1116
          Unresolved non-hydrogen angles: 1417
          Unresolved non-hydrogen dihedrals: 886
          Unresolved non-hydrogen chiralities: 125
          Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 17, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 35, 'ARG:plan': 30}
          Unresolved non-hydrogen planarities: 599
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.40, per 1000 atoms: 0.71
  Number of scatterers: 6164
  At special positions: 0
  Unit cell: (78.048, 109.484, 128.996, 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       9     16.00
     P       6     15.00
     O    1197      8.00
     N    1170      7.00
     C    3782      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM 6126  O3A ATP A1101 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1944

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 8 sheets defined
      46.0% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 466 through 473
    Processing helix  chain 'A' and resid 545 through 557
    Processing helix  chain 'A' and resid 587 through 594
    Processing helix  chain 'A' and resid 600 through 620
    Processing helix  chain 'A' and resid 659 through 666
      removed outlier: 3.556A  pdb=" N   THR A 662 " --> pdb=" O   GLN A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 703
    Processing helix  chain 'A' and resid 715 through 726
      removed outlier: 4.088A  pdb=" N   GLY A 726 " --> pdb=" O   ARG A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 753
      removed outlier: 3.655A  pdb=" N   GLY A 745 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ALA A 753 " --> pdb=" O   GLN A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 773
    Processing helix  chain 'A' and resid 774 through 776
      No H-bonds generated for 'chain 'A' and resid 774 through 776'
    Processing helix  chain 'A' and resid 781 through 818
      removed outlier: 4.537A  pdb=" N   LEU A 785 " --> pdb=" O   LEU A 781 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU A 817 " --> pdb=" O   ALA A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 830
      removed outlier: 3.580A  pdb=" N   ALA A 826 " --> pdb=" O   PRO A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 861
      removed outlier: 4.446A  pdb=" N   THR A 861 " --> pdb=" O   SER A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 881
    Processing helix  chain 'A' and resid 907 through 924
      removed outlier: 3.500A  pdb=" N   CYS A 911 " --> pdb=" O   ARG A 907 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU A 918 " --> pdb=" O   ALA A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 975
    Processing helix  chain 'A' and resid 985 through 996
      removed outlier: 3.502A  pdb=" N   GLY A 996 " --> pdb=" O   LEU A 992 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 483
    Processing helix  chain 'B' and resid 545 through 558
      removed outlier: 3.895A  pdb=" N   VAL B 558 " --> pdb=" O   HIS B 554 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 594
    Processing helix  chain 'B' and resid 600 through 620
      removed outlier: 3.752A  pdb=" N   HIS B 619 " --> pdb=" O   MET B 615 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASN B 620 " --> pdb=" O   LEU B 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 634
    Processing helix  chain 'B' and resid 660 through 667
      removed outlier: 4.327A  pdb=" N   LYS B 667 " --> pdb=" O   VAL B 663 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 671 through 676
    Processing helix  chain 'B' and resid 685 through 702
      removed outlier: 3.928A  pdb=" N   LEU B 702 " --> pdb=" O   GLN B 698 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 715 through 725
    Processing helix  chain 'B' and resid 741 through 752
      removed outlier: 3.595A  pdb=" N   TRP B 752 " --> pdb=" O   MET B 748 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 773
    Processing helix  chain 'B' and resid 779 through 821
      removed outlier: 3.749A  pdb=" N   ASN B 783 " --> pdb=" O   ASN B 779 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   LEU B 784 " --> pdb=" O   ILE B 780 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU B 821 " --> pdb=" O   LEU B 817 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 822 through 831
      removed outlier: 3.649A  pdb=" N   ARG B 831 " --> pdb=" O   GLU B 827 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 852 through 860
    Processing helix  chain 'B' and resid 861 through 880
      removed outlier: 3.768A  pdb=" N   THR B 867 " --> pdb=" O   MET B 863 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL B 879 " --> pdb=" O   CYS B 875 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 908 through 926
      removed outlier: 4.053A  pdb=" N   VAL B 913 " --> pdb=" O   HIS B 909 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 914 " --> pdb=" O   ALA B 910 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LEU B 921 " --> pdb=" O   ALA B 917 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ASP B 922 " --> pdb=" O   LEU B 918 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER B 926 " --> pdb=" O   ASP B 922 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 964 through 976
      removed outlier: 4.047A  pdb=" N   ASN B 976 " --> pdb=" O   ARG B 972 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 986 through 995
      removed outlier: 3.764A  pdb=" N   VAL B 991 " --> pdb=" O   GLU B 987 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 524 through 527
      removed outlier: 3.673A  pdb=" N   LYS A 535 " --> pdb=" O   ILE A 578 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   CYS A 577 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ALA A 569 " --> pdb=" O   CYS A 577 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   LEU A 579 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 635 through 636
    Processing sheet with id=AA3, first strand: chain 'A' and resid 886 through 889
      removed outlier: 4.645A  pdb=" N   LYS A 887 " --> pdb=" O   VAL A 898 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   VAL A 898 " --> pdb=" O   LYS A 887 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 847 " --> pdb=" O   GLY A 942 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 949 through 953
    Processing sheet with id=AA5, first strand: chain 'A' and resid 999 through 1008
      removed outlier: 7.543A  pdb=" N   LEU A1000 " --> pdb=" O   LEU A1020 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   LEU A1020 " --> pdb=" O   LEU A1000 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   LEU A1002 " --> pdb=" O   TRP A1018 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   TRP A1018 " --> pdb=" O   LEU A1002 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 525 through 526
      removed outlier: 7.070A  pdb=" N   LEU B 579 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 838 through 839
    Processing sheet with id=AA8, first strand: chain 'B' and resid 886 through 891
      removed outlier: 7.972A  pdb=" N   MET B 896 " --> pdb=" O   VAL B 888 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   THR B 890 " --> pdb=" O   ALA B 894 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   ALA B 894 " --> pdb=" O   THR B 890 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   SER B 848 " --> pdb=" O   TYR B 895 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL B 897 " --> pdb=" O   TYR B 846 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP B 849 " --> pdb=" O   ARG B 940 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ARG B 940 " --> pdb=" O   ASP B 849 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   THR B 945 " --> pdb=" O   SER B 985 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   GLY B1012 " --> pdb=" O   GLU B1007 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU B1007 " --> pdb=" O   GLY B1012 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   VAL B1014 " --> pdb=" O   ASP B1005 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ASP B1005 " --> pdb=" O   VAL B1014 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   THR B1016 " --> pdb=" O   ARG B1003 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1065 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: 1.80

  Time building geometry restraints manager: 2.06 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: 2209
        1.34 -     1.45: 621
        1.45 -     1.57: 3412
        1.57 -     1.69: 10
        1.69 -     1.81: 15
  Bond restraints: 6267
  Sorted by residual:
  bond pdb=" C4  ATP B1101 "
       pdb=" C5  ATP B1101 "
    ideal  model  delta    sigma   weight residual
    1.388  1.463 -0.075 1.00e-02 1.00e+04 5.61e+01
  bond pdb=" C4  ATP A1101 "
       pdb=" C5  ATP A1101 "
    ideal  model  delta    sigma   weight residual
    1.388  1.460 -0.072 1.00e-02 1.00e+04 5.25e+01
  bond pdb=" C5  ATP B1101 "
       pdb=" C6  ATP B1101 "
    ideal  model  delta    sigma   weight residual
    1.409  1.474 -0.065 1.00e-02 1.00e+04 4.28e+01
  bond pdb=" C5  ATP A1101 "
       pdb=" C6  ATP A1101 "
    ideal  model  delta    sigma   weight residual
    1.409  1.472 -0.063 1.00e-02 1.00e+04 3.99e+01
  bond pdb=" C5  ATP B1101 "
       pdb=" N7  ATP B1101 "
    ideal  model  delta    sigma   weight residual
    1.387  1.339  0.048 1.00e-02 1.00e+04 2.31e+01
  ... (remaining 6262 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.71: 8641
        4.71 -     9.41: 23
        9.41 -    14.12: 0
       14.12 -    18.82: 1
       18.82 -    23.53: 3
  Bond angle restraints: 8668
  Sorted by residual:
  angle pdb=" PB  ATP A1101 "
        pdb=" O3B ATP A1101 "
        pdb=" PG  ATP A1101 "
      ideal   model   delta    sigma   weight residual
     139.87  116.34   23.53 1.00e+00 1.00e+00 5.53e+02
  angle pdb=" PB  ATP B1101 "
        pdb=" O3B ATP B1101 "
        pdb=" PG  ATP B1101 "
      ideal   model   delta    sigma   weight residual
     139.87  119.21   20.66 1.00e+00 1.00e+00 4.27e+02
  angle pdb=" PA  ATP A1101 "
        pdb=" O3A ATP A1101 "
        pdb=" PB  ATP A1101 "
      ideal   model   delta    sigma   weight residual
     136.83  117.74   19.09 1.00e+00 1.00e+00 3.64e+02
  angle pdb=" PA  ATP B1101 "
        pdb=" O3A ATP B1101 "
        pdb=" PB  ATP B1101 "
      ideal   model   delta    sigma   weight residual
     136.83  121.07   15.76 1.00e+00 1.00e+00 2.48e+02
  angle pdb=" C5  ATP B1101 "
        pdb=" C4  ATP B1101 "
        pdb=" N3  ATP B1101 "
      ideal   model   delta    sigma   weight residual
     126.80  119.08    7.72 1.00e+00 1.00e+00 5.96e+01
  ... (remaining 8663 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3513
       17.99 -    35.98: 132
       35.98 -    53.96: 35
       53.96 -    71.95: 11
       71.95 -    89.94: 5
  Dihedral angle restraints: 3696
    sinusoidal: 702
      harmonic: 2994
  Sorted by residual:
  dihedral pdb=" CA  ILE B 644 "
           pdb=" C   ILE B 644 "
           pdb=" N   THR B 645 "
           pdb=" CA  THR B 645 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.02  -20.98     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  ARG B 759 "
           pdb=" C   ARG B 759 "
           pdb=" N   PRO B 760 "
           pdb=" CA  PRO B 760 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.17  -20.83     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  GLY B 529 "
           pdb=" C   GLY B 529 "
           pdb=" N   ASN B 530 "
           pdb=" CA  ASN B 530 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.57   20.43     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 3693 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 918
       0.076 -    0.152: 107
       0.152 -    0.228: 6
       0.228 -    0.303: 1
       0.303 -    0.379: 2
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CA  THR A1016 "
            pdb=" N   THR A1016 "
            pdb=" C   THR A1016 "
            pdb=" CB  THR A1016 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.15    0.38 2.00e-01 2.50e+01 3.59e+00
  chirality pdb=" CA  HIS A 944 "
            pdb=" N   HIS A 944 "
            pdb=" C   HIS A 944 "
            pdb=" CB  HIS A 944 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CA  VAL B 682 "
            pdb=" N   VAL B 682 "
            pdb=" C   VAL B 682 "
            pdb=" CB  VAL B 682 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 1031 not shown)

  Planarity restraints: 1208
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 572 "   -0.060 5.00e-02 4.00e+02   8.93e-02 1.28e+01
        pdb=" N   PRO A 573 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO A 573 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 573 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 772 "    0.019 2.00e-02 2.50e+03   1.84e-02 5.92e+00
        pdb=" CG  PHE B 772 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 772 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 772 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 772 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 772 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 772 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 484 "    0.036 5.00e-02 4.00e+02   5.45e-02 4.75e+00
        pdb=" N   PRO B 485 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 485 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 485 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1205 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 124
        2.66 -     3.22: 6433
        3.22 -     3.78: 8702
        3.78 -     4.34: 9848
        4.34 -     4.90: 15368
  Nonbonded interactions: 40475
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 633 "
            pdb=" O1G ATP A1101 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" NZ  LYS A 535 "
            pdb=" O3A ATP A1101 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" ND2 ASN B 633 "
            pdb=" O2B ATP B1101 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   ASN A 628 "
            pdb=" OD1 ASN A 628 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ASN A 773 "
            pdb=" N   SER A 777 "
     model   vdw
     2.285 3.120
  ... (remaining 40470 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 469 through 482 or (resid 483 through 484 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 485 through 486 or (resid 523  \ 
through 525 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 
6 through 530 or (resid 531 through 533 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 534 through 537 or (resid 538 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 539 through 541 or (resid 542 through  \ 
549 and (name N or name CA or name C or name O or name CB )) or resid 550 throug \ 
h 558 or (resid 559 through 561 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 562 through 565 or (resid 566 through 567 and (name N or name  \ 
CA or name C or name O or name CB )) or (resid 568 through 572 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 573 through 587 or (resid 588 t \ 
hrough 600 and (name N or name CA or name C or name O or name CB )) or resid 601 \ 
 through 615 or (resid 616 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 617 through 619 or (resid 620 and (name N or name CA or name C or n \ 
ame O or name CB )) or (resid 621 through 625 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 626 through 629 or (resid 630 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 631 through 638 or (resid 639 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 640 through 641  \ 
or (resid 642 through 646 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 647 through 651 or (resid 652 through 653 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 654 through 655 or (resid 656 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 657 through 662 or (resi \ 
d 663 through 668 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 669 through 678 or (resid 679 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 680 through 682 or (resid 683 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 684 or (resid 685 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 686 through 694 or (resid 695 through 70 \ 
4 and (name N or name CA or name C or name O or name CB )) or resid 705 through  \ 
707 or (resid 708 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 709 through 714 or (resid 715 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 716 through 783 or (resid 784 through 787 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 788 through 794 or (resid 795 th \ 
rough 801 and (name N or name CA or name C or name O or name CB )) or resid 802  \ 
through 803 or (resid 804 through 805 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 806 or (resid 807 through 808 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 809 through 819 or (resid 820 through 82 \ 
1 and (name N or name CA or name C or name O or name CB )) or resid 822 through  \ 
858 or (resid 859 through 861 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 862 through 869 or (resid 870 through 891 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 892 or (resid 893 through 899 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 900 through 915 or ( \ 
resid 916 through 932 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 933 through 1021 or resid 1101))
  selection = (chain 'B' and ((resid 469 through 478 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 479 through 526 or (resid 527 through 528 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 529 through 535 or (resid 5 \ 
36 through 538 and (name N or name CA or name C or name O or name CB )) or resid \ 
 539 through 557 or (resid 558 through 561 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 562 through 563 or (resid 564 and (name N or name C \ 
A or name C or name O or name CB )) or resid 565 through 589 or (resid 590 throu \ 
gh 600 and (name N or name CA or name C or name O or name CB )) or resid 601 thr \ 
ough 603 or (resid 604 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 605 through 608 or (resid 609 through 613 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 614 through 618 or (resid 619 through 620 a \ 
nd (name N or name CA or name C or name O or name CB )) or (resid 621 through 62 \ 
5 and (name N or name CA or name C or name O or name CB )) or resid 626 through  \ 
628 or (resid 629 through 630 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 631 or (resid 632 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 633 or (resid 634 through 635 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 636 through 640 or (resid 641 through 646 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 647 through 654  \ 
or (resid 655 through 656 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 657 through 666 or (resid 667 through 668 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 669 or (resid 670 through 671 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 672 through 698 or (resi \ 
d 699 through 704 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 707 through 712 or (resid 713 through 715 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 716 through 730 or (resid 731 through 732 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 733 or (resid 73 \ 
4 through 743 and (name N or name CA or name C or name O or name CB )) or resid  \ 
744 through 746 or (resid 747 through 748 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 749 or (resid 750 through 751 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 752 through 753 or (resid 754 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 755 through 756 or ( \ 
resid 757 through 759 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 760 through 762 or (resid 763 through 787 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 788 through 792 or (resid 793 through 801 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 802 through 809  \ 
or (resid 810 through 821 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 822 through 856 or (resid 857 through 861 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 862 through 870 or (resid 871 through 89 \ 
1 and (name N or name CA or name C or name O or name CB )) or (resid 892 through \ 
 899 and (name N or name CA or name C or name O or name CB )) or resid 900 throu \ 
gh 908 or (resid 909 through 932 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 933 through 946 or (resid 947 through 950 and (name N or name \ 
 CA or name C or name O or name CB )) or (resid 951 through 976 and (name N or n \ 
ame CA or name C or name O or name CB )) or (resid 977 through 995 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 996 through 997 or (resid 9 \ 
98 through 1003 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 1004 through 1021 or resid 1101))
}

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:             1.160
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.620
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
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      :  0.005   0.075   6267  Z= 0.363
  Angle     :  0.876  23.527   8668  Z= 0.663
  Chirality :  0.048   0.379   1034
  Planarity :  0.005   0.089   1208
  Dihedral  : 12.776  89.939   1752
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.10 %
  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: -1.99 (0.25), residues: 1030
  helix:  0.14 (0.24), residues: 437
  sheet: -1.51 (0.45), residues: 129
  loop : -2.77 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 480 
 HIS   0.007   0.002   HIS A 708 
 PHE   0.043   0.003   PHE B 772 
 TYR   0.014   0.002   TYR A 605 
 ARG   0.008   0.001   ARG B 585 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  809 GLU cc_start: 0.8515 (tp30) cc_final: 0.8251 (tp30)
REVERT: A  870 ASN cc_start: 0.8958 (t0) cc_final: 0.8308 (m110)
REVERT: B  634 CYS cc_start: 0.6137 (p) cc_final: 0.5810 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1992
  time to fit residues: 27.2000
Evaluate side-chains
  65 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 628 ASN
A 633 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.120918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.099577 restraints weight = 23606.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.101096 restraints weight = 17557.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.102355 restraints weight = 13982.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6267  Z= 0.213
  Angle     :  0.565   5.965   8668  Z= 0.320
  Chirality :  0.043   0.151   1034
  Planarity :  0.005   0.057   1208
  Dihedral  : 11.014  86.579   1137
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  3.42 %
    Favored  : 96.20 %
  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: -0.85 (0.26), residues: 1030
  helix:  1.31 (0.25), residues: 437
  sheet: -0.54 (0.50), residues: 107
  loop : -2.46 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 480 
 HIS   0.005   0.001   HIS B 562 
 PHE   0.038   0.003   PHE B 772 
 TYR   0.016   0.002   TYR A 605 
 ARG   0.008   0.001   ARG B 585 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A  870 ASN cc_start: 0.9044 (t0) cc_final: 0.8404 (m-40)
REVERT: B  634 CYS cc_start: 0.6723 (p) cc_final: 0.6395 (p)
REVERT: B  647 TYR cc_start: 0.7792 (p90) cc_final: 0.7513 (p90)
REVERT: B  757 GLN cc_start: 0.8122 (pp30) cc_final: 0.7760 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1752
  time to fit residues: 22.0434
Evaluate side-chains
  64 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 93 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0370
   chunk 49 optimal weight:   20.0000
   chunk 73 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 90 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 85 optimal weight:   20.0000
   overall best weight:    0.9862

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.121833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.100293 restraints weight = 23352.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.101772 restraints weight = 17439.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.103052 restraints weight = 13917.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6267  Z= 0.161
  Angle     :  0.502   6.572   8668  Z= 0.278
  Chirality :  0.041   0.122   1034
  Planarity :  0.004   0.053   1208
  Dihedral  : 10.145  84.507   1137
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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: -0.14 (0.27), residues: 1030
  helix:  1.89 (0.25), residues: 442
  sheet: -0.19 (0.54), residues: 100
  loop : -2.08 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 601 
 HIS   0.004   0.001   HIS A 708 
 PHE   0.024   0.002   PHE B 772 
 TYR   0.012   0.001   TYR A 582 
 ARG   0.003   0.001   ARG B 536 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  870 ASN cc_start: 0.9037 (t0) cc_final: 0.8406 (m-40)
REVERT: B  634 CYS cc_start: 0.6607 (p) cc_final: 0.6153 (p)
REVERT: B  647 TYR cc_start: 0.7911 (p90) cc_final: 0.7586 (p90)
REVERT: B  757 GLN cc_start: 0.7955 (pp30) cc_final: 0.7605 (pp30)
REVERT: B  763 GLN cc_start: 0.8356 (mp10) cc_final: 0.8139 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1787
  time to fit residues: 20.1408
Evaluate side-chains
  64 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0670
   chunk 64 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 18 optimal weight:    0.2980
   chunk 96 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   overall best weight:    1.8522

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.117385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.095713 restraints weight = 23796.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.097290 restraints weight = 17938.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.098331 restraints weight = 14281.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6267  Z= 0.224
  Angle     :  0.542   5.640   8668  Z= 0.304
  Chirality :  0.042   0.138   1034
  Planarity :  0.004   0.049   1208
  Dihedral  :  9.971  79.748   1137
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  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: -0.29 (0.26), residues: 1030
  helix:  1.75 (0.25), residues: 443
  sheet: -0.44 (0.52), residues: 102
  loop : -2.11 (0.26), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 480 
 HIS   0.008   0.002   HIS B 562 
 PHE   0.022   0.003   PHE B 707 
 TYR   0.017   0.002   TYR A 605 
 ARG   0.005   0.000   ARG A 683 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  870 ASN cc_start: 0.8941 (t0) cc_final: 0.8375 (m-40)
REVERT: B  634 CYS cc_start: 0.6639 (p) cc_final: 0.6410 (p)
REVERT: B  647 TYR cc_start: 0.8025 (p90) cc_final: 0.7675 (p90)
REVERT: B  763 GLN cc_start: 0.8373 (mp10) cc_final: 0.8129 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1833
  time to fit residues: 19.0565
Evaluate side-chains
  62 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 8 optimal weight:    0.0040
   chunk 68 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 73 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 90 optimal weight:   20.0000
   chunk 51 optimal weight:   30.0000
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.3794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.120404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.099873 restraints weight = 24149.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.101209 restraints weight = 18823.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.102202 restraints weight = 15349.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6267  Z= 0.175
  Angle     :  0.505   7.726   8668  Z= 0.275
  Chirality :  0.042   0.170   1034
  Planarity :  0.004   0.048   1208
  Dihedral  :  8.981  57.944   1137
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  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:  0.02 (0.27), residues: 1030
  helix:  2.10 (0.25), residues: 444
  sheet: -0.57 (0.52), residues: 102
  loop : -1.98 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 480 
 HIS   0.004   0.001   HIS B 562 
 PHE   0.019   0.002   PHE A 550 
 TYR   0.017   0.001   TYR A 605 
 ARG   0.004   0.001   ARG A 683 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  870 ASN cc_start: 0.8970 (t0) cc_final: 0.8418 (m-40)
REVERT: A  876 PHE cc_start: 0.7763 (m-80) cc_final: 0.7427 (m-80)
REVERT: B  592 LEU cc_start: 0.7715 (tt) cc_final: 0.7256 (mm)
REVERT: B  634 CYS cc_start: 0.6657 (p) cc_final: 0.6344 (p)
REVERT: B  647 TYR cc_start: 0.8055 (p90) cc_final: 0.7792 (p90)
REVERT: B  750 ARG cc_start: 0.8615 (mmp80) cc_final: 0.8309 (ttm-80)
REVERT: B  763 GLN cc_start: 0.8314 (mp10) cc_final: 0.8046 (mp10)
REVERT: B  802 ARG cc_start: 0.8976 (mmp80) cc_final: 0.8729 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1728
  time to fit residues: 18.3450
Evaluate side-chains
  67 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 48 optimal weight:   20.0000
   chunk 4 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0670
   chunk 38 optimal weight:    9.9990
   overall best weight:    1.2920

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.119973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.099715 restraints weight = 23491.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.100913 restraints weight = 18389.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.101888 restraints weight = 15170.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6267  Z= 0.173
  Angle     :  0.495   7.665   8668  Z= 0.268
  Chirality :  0.041   0.128   1034
  Planarity :  0.004   0.048   1208
  Dihedral  :  8.442  63.936   1137
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  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:  0.19 (0.27), residues: 1030
  helix:  2.24 (0.25), residues: 444
  sheet: -0.41 (0.52), residues: 110
  loop : -1.93 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 480 
 HIS   0.004   0.001   HIS B 562 
 PHE   0.018   0.002   PHE A 693 
 TYR   0.019   0.001   TYR A 605 
 ARG   0.003   0.000   ARG B 802 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  640 PHE cc_start: 0.6622 (t80) cc_final: 0.6172 (t80)
REVERT: A  870 ASN cc_start: 0.9004 (t0) cc_final: 0.8402 (m-40)
REVERT: B  634 CYS cc_start: 0.6636 (p) cc_final: 0.6379 (p)
REVERT: B  647 TYR cc_start: 0.8086 (p90) cc_final: 0.7834 (p90)
REVERT: B  763 GLN cc_start: 0.8311 (mp10) cc_final: 0.8030 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1802
  time to fit residues: 19.7767
Evaluate side-chains
  69 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 98 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0670
   chunk 95 optimal weight:    9.9990
   chunk 88 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0270
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 620 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.120175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.098753 restraints weight = 22809.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.100368 restraints weight = 17339.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.101523 restraints weight = 13866.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6267  Z= 0.140
  Angle     :  0.480   8.904   8668  Z= 0.256
  Chirality :  0.040   0.129   1034
  Planarity :  0.004   0.047   1208
  Dihedral  :  7.843  79.362   1137
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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:  0.38 (0.28), residues: 1030
  helix:  2.41 (0.25), residues: 448
  sheet: -0.38 (0.52), residues: 110
  loop : -1.87 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 480 
 HIS   0.002   0.001   HIS B 562 
 PHE   0.027   0.002   PHE A 550 
 TYR   0.022   0.001   TYR A 605 
 ARG   0.004   0.000   ARG B 802 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 TYR cc_start: 0.7602 (m-80) cc_final: 0.7345 (m-80)
REVERT: A  752 TRP cc_start: 0.7409 (m-10) cc_final: 0.7086 (m-10)
REVERT: A  790 GLN cc_start: 0.7862 (tp40) cc_final: 0.7574 (tp40)
REVERT: A  870 ASN cc_start: 0.8960 (t0) cc_final: 0.8392 (m-40)
REVERT: B  475 LEU cc_start: 0.6935 (mm) cc_final: 0.6733 (tt)
REVERT: B  647 TYR cc_start: 0.8105 (p90) cc_final: 0.7815 (p90)
REVERT: B  757 GLN cc_start: 0.8192 (pp30) cc_final: 0.7914 (pp30)
REVERT: B  763 GLN cc_start: 0.8262 (mp10) cc_final: 0.7976 (mp10)
REVERT: B  802 ARG cc_start: 0.8974 (mmp80) cc_final: 0.8713 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1830
  time to fit residues: 19.9214
Evaluate side-chains
  69 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 60 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 86 optimal weight:   30.0000
   chunk 58 optimal weight:    9.9990
   chunk 43 optimal weight:   20.0000
   chunk 40 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0050
   chunk 101 optimal weight:    6.9990
   chunk 83 optimal weight:    0.2980
   overall best weight:    1.5598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.117585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.096106 restraints weight = 23174.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.097655 restraints weight = 17786.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.098681 restraints weight = 14333.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6267  Z= 0.192
  Angle     :  0.512   8.775   8668  Z= 0.278
  Chirality :  0.041   0.127   1034
  Planarity :  0.004   0.046   1208
  Dihedral  :  7.579  78.052   1137
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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:  0.27 (0.27), residues: 1030
  helix:  2.29 (0.25), residues: 443
  sheet: -0.41 (0.52), residues: 110
  loop : -1.84 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 480 
 HIS   0.005   0.001   HIS B 562 
 PHE   0.017   0.002   PHE A 707 
 TYR   0.022   0.002   TYR A 605 
 ARG   0.003   0.000   ARG B 802 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 TYR cc_start: 0.7577 (m-80) cc_final: 0.7300 (m-80)
REVERT: A  870 ASN cc_start: 0.8944 (t0) cc_final: 0.8422 (m-40)
REVERT: B  647 TYR cc_start: 0.8148 (p90) cc_final: 0.7947 (p90)
REVERT: B  763 GLN cc_start: 0.8252 (mp10) cc_final: 0.7964 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1857
  time to fit residues: 19.8486
Evaluate side-chains
  67 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0970
   chunk 53 optimal weight:    8.9990
   chunk 102 optimal weight:   40.0000
   chunk 92 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 17 optimal weight:    0.3980
   chunk 83 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    3.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.115025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.094968 restraints weight = 24188.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.096040 restraints weight = 19500.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.096782 restraints weight = 16449.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.4563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6267  Z= 0.316
  Angle     :  0.601   7.788   8668  Z= 0.336
  Chirality :  0.043   0.133   1034
  Planarity :  0.005   0.046   1208
  Dihedral  :  8.294  71.067   1137
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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: -0.53 (0.26), residues: 1030
  helix:  1.51 (0.25), residues: 440
  sheet: -0.75 (0.51), residues: 109
  loop : -2.14 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP B 480 
 HIS   0.009   0.002   HIS B 562 
 PHE   0.025   0.003   PHE A 707 
 TYR   0.024   0.002   TYR A 605 
 ARG   0.004   0.001   ARG B 536 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
REVERT: A  870 ASN cc_start: 0.8990 (t0) cc_final: 0.8466 (m-40)
REVERT: B  763 GLN cc_start: 0.8321 (mp10) cc_final: 0.8021 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1698
  time to fit residues: 16.3536
Evaluate side-chains
  60 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 101 optimal weight:    8.9990
   chunk 58 optimal weight:    4.9990
   chunk 99 optimal weight:   20.0000
   chunk 102 optimal weight:   20.0000
   chunk 14 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 44 optimal weight:   30.0000
   chunk 24 optimal weight:    6.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    2.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.116151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.096243 restraints weight = 24193.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.097338 restraints weight = 19494.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.098244 restraints weight = 16364.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.4760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6267  Z= 0.253
  Angle     :  0.560   8.685   8668  Z= 0.307
  Chirality :  0.042   0.131   1034
  Planarity :  0.004   0.047   1208
  Dihedral  :  7.945  68.519   1137
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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: -0.40 (0.27), residues: 1030
  helix:  1.64 (0.25), residues: 440
  sheet: -0.75 (0.51), residues: 107
  loop : -2.07 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 480 
 HIS   0.006   0.001   HIS A 708 
 PHE   0.024   0.003   PHE A 550 
 TYR   0.020   0.002   TYR A 605 
 ARG   0.004   0.001   ARG B 536 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  870 ASN cc_start: 0.8995 (t0) cc_final: 0.8475 (m-40)
REVERT: B  763 GLN cc_start: 0.8252 (mp10) cc_final: 0.7957 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1535
  time to fit residues: 15.3815
Evaluate side-chains
  62 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 51 optimal weight:   30.0000
   chunk 77 optimal weight:    0.1980
   chunk 39 optimal weight:    9.9990
   chunk 95 optimal weight:   30.0000
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.117255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.096020 restraints weight = 23997.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.097510 restraints weight = 18461.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.098676 restraints weight = 14910.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6267  Z= 0.169
  Angle     :  0.518   9.301   8668  Z= 0.275
  Chirality :  0.041   0.132   1034
  Planarity :  0.004   0.047   1208
  Dihedral  :  7.356  66.111   1137
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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: -0.07 (0.27), residues: 1030
  helix:  2.06 (0.25), residues: 449
  sheet: -0.86 (0.49), residues: 119
  loop : -2.09 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 601 
 HIS   0.004   0.001   HIS B 562 
 PHE   0.024   0.002   PHE A 550 
 TYR   0.018   0.001   TYR A 605 
 ARG   0.004   0.001   ARG B 750 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1836.51 seconds
wall clock time: 33 minutes 55.19 seconds (2035.19 seconds total)