Starting phenix.real_space_refine
on Sat Aug 23 07:15:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iby_35349/08_2025/8iby_35349.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iby_35349/08_2025/8iby_35349.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2025/8iby_35349.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2025/8iby_35349.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2025/8iby_35349.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iby_35349/08_2025/8iby_35349.cif"
  }
  resolution = 3.47
  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
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=   0.010 sd=   0.085
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     198      5.49       5
     S      32      5.16       5
     C    5817      2.51       5
     N    1973      2.21       5
     O    2482      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10503
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 4233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 4233
          Classifications: {'RNA': 198}
          Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 17, 'rna3p_pur': 91, 'rna3p_pyr': 75}
          Link IDs: {'rna2p': 32, 'rna3p': 165}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 6269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 793, 6269
          Classifications: {'peptide': 793}
          Link IDs: {'PTRANS': 39, 'TRANS': 753}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9132  SG  CYS C 934      59.637  71.301  25.232  1.00104.66           S
  ATOM   9158  SG  CYS C 938      58.180  73.110  22.172  1.00109.37           S
  ATOM   9263  SG  CYS C 951      55.829  71.305  24.654  1.00 93.60           S

  Time building chain proxies: 2.36, per 1000 atoms: 0.22
  Number of scatterers: 10503
  At special positions: 0
  Unit cell: (107.594, 130.65, 119.671, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      32     16.00
     P     198     15.00
     O    2482      8.00
     N    1973      7.00
     C    5817      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 384.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C1201 "
        pdb="ZN    ZN C1201 " - pdb=" NE2 HIS C 946 "
        pdb="ZN    ZN C1201 " - pdb=" SG  CYS C 934 "
        pdb="ZN    ZN C1201 " - pdb=" SG  CYS C 938 "
        pdb="ZN    ZN C1201 " - pdb=" SG  CYS C 951 "
      Number of angles added : 3


  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 8 sheets defined
      54.6% alpha, 10.5% beta
      57 base pairs and 88 stacking pairs defined.
    Time for finding SS restraints: 1.50
  Creating SS restraints...
    Processing helix  chain 'C' and resid 305 through 324
    Processing helix  chain 'C' and resid 324 through 335
      removed outlier: 3.553A  pdb=" N   ALA C 328 " --> pdb=" O   CYS C 324 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASP C 334 " --> pdb=" O   ALA C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 352
    Processing helix  chain 'C' and resid 365 through 373
    Processing helix  chain 'C' and resid 393 through 399
      removed outlier: 3.928A  pdb=" N   LYS C 397 " --> pdb=" O   VAL C 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 414 through 420
      removed outlier: 3.937A  pdb=" N   VAL C 420 " --> pdb=" O   GLN C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 436
    Processing helix  chain 'C' and resid 439 through 444
    Processing helix  chain 'C' and resid 458 through 460
      No H-bonds generated for 'chain 'C' and resid 458 through 460'
    Processing helix  chain 'C' and resid 469 through 487
      removed outlier: 3.577A  pdb=" N   ILE C 478 " --> pdb=" O   HIS C 474 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU C 479 " --> pdb=" O   PHE C 475 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 504 through 519
    Processing helix  chain 'C' and resid 539 through 549
    Processing helix  chain 'C' and resid 552 through 565
    Processing helix  chain 'C' and resid 592 through 607
      removed outlier: 3.628A  pdb=" N   ASN C 598 " --> pdb=" O   PRO C 594 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 636 through 655
      removed outlier: 3.624A  pdb=" N   MET C 640 " --> pdb=" O   SER C 636 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLN C 641 " --> pdb=" O   LYS C 637 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLU C 642 " --> pdb=" O   VAL C 638 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER C 643 " --> pdb=" O   GLY C 639 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 719 through 730
    Processing helix  chain 'C' and resid 733 through 744
    Processing helix  chain 'C' and resid 745 through 750
      removed outlier: 3.564A  pdb=" N   GLN C 750 " --> pdb=" O   ILE C 746 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 751 through 755
      removed outlier: 3.884A  pdb=" N   LEU C 755 " --> pdb=" O   GLY C 752 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 759 through 779
      removed outlier: 3.802A  pdb=" N   LEU C 763 " --> pdb=" O   SER C 759 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 786 through 791
      removed outlier: 4.177A  pdb=" N   HIS C 790 " --> pdb=" O   LYS C 786 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 802 through 816
      removed outlier: 3.740A  pdb=" N   ILE C 807 " --> pdb=" O   VAL C 803 " (cutoff:3.500A)
      Proline residue:  C 808  - end of helix
    Processing helix  chain 'C' and resid 817 through 821
    Processing helix  chain 'C' and resid 823 through 831
      removed outlier: 3.508A  pdb=" N   ARG C 827 " --> pdb=" O   TRP C 823 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LYS C 831 " --> pdb=" O   ARG C 827 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 833 through 849
    Processing helix  chain 'C' and resid 861 through 871
    Processing helix  chain 'C' and resid 875 through 879
    Processing helix  chain 'C' and resid 884 through 889
      removed outlier: 3.590A  pdb=" N   THR C 888 " --> pdb=" O   PRO C 885 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 899 through 911
      removed outlier: 3.679A  pdb=" N   VAL C 904 " --> pdb=" O   GLY C 900 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 918 through 922
      removed outlier: 3.821A  pdb=" N   ARG C 922 " --> pdb=" O   ARG C 919 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 928 through 932
    Processing helix  chain 'C' and resid 943 through 950
    Processing helix  chain 'C' and resid 951 through 953
      No H-bonds generated for 'chain 'C' and resid 951 through 953'
    Processing helix  chain 'C' and resid 954 through 976
    Processing helix  chain 'C' and resid 1018 through 1032
      removed outlier: 3.736A  pdb=" N   LYS C1026 " --> pdb=" O   LEU C1022 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LYS C1029 " --> pdb=" O   GLU C1025 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1035 through 1045
    Processing helix  chain 'C' and resid 1066 through 1077
      removed outlier: 3.710A  pdb=" N   ILE C1077 " --> pdb=" O   LEU C1073 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1080 through 1105
      removed outlier: 3.819A  pdb=" N   LEU C1084 " --> pdb=" O   ARG C1080 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL C1087 " --> pdb=" O   THR C1083 " (cutoff:3.500A)
      Proline residue:  C1088  - end of helix
      removed outlier: 4.317A  pdb=" N   MET C1105 " --> pdb=" O   ARG C1101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 467
    Processing sheet with id=AA2, first strand: chain 'C' and resid 623 through 624
      removed outlier: 3.736A  pdb=" N   VAL C 631 " --> pdb=" O   LEU C 624 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU C 528 " --> pdb=" O   LEU C 630 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 623 through 624
      removed outlier: 3.736A  pdb=" N   VAL C 631 " --> pdb=" O   LEU C 624 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU C 528 " --> pdb=" O   LEU C 630 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 537 through 538
      removed outlier: 4.429A  pdb=" N   VAL C 537 " --> pdb=" O   GLY C 585 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 614 through 616
    Processing sheet with id=AA6, first strand: chain 'C' and resid 686 through 687
    Processing sheet with id=AA7, first strand: chain 'C' and resid 851 through 852
    Processing sheet with id=AA8, first strand: chain 'C' and resid 979 through 982
      removed outlier: 3.762A  pdb=" N   THR C 979 " --> pdb=" O   SER C1000 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER C1000 " --> pdb=" O   THR C 979 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   GLY C1005 " --> pdb=" O   ARG C1053 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   THR C1055 " --> pdb=" O   GLY C1005 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   ILE C1007 " --> pdb=" O   THR C1055 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   CYS C1057 " --> pdb=" O   ILE C1007 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASP C1009 " --> pdb=" O   CYS C1057 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   ILE C1059 " --> pdb=" O   ASP C1009 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   GLN C1011 " --> pdb=" O   ILE C1059 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL C1064 " --> pdb=" O   SER C1060 " (cutoff:3.500A)

    308 hydrogen bonds defined for protein.
    861 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      148 hydrogen bonds
      272 hydrogen bond angles
      0 basepair planarities
      57 basepair parallelities
      88 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.11 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: 2787
        1.34 -     1.46: 3602
        1.46 -     1.58: 4301
        1.58 -     1.70: 394
        1.70 -     1.83: 46
  Bond restraints: 11130
  Sorted by residual:
  bond pdb=" CB  PRO C 366 "
       pdb=" CG  PRO C 366 "
    ideal  model  delta    sigma   weight residual
    1.492  1.616 -0.124 5.00e-02 4.00e+02 6.17e+00
  bond pdb=" CB  PRO C 915 "
       pdb=" CG  PRO C 915 "
    ideal  model  delta    sigma   weight residual
    1.492  1.595 -0.103 5.00e-02 4.00e+02 4.27e+00
  bond pdb=" CG1 ILE C 959 "
       pdb=" CD1 ILE C 959 "
    ideal  model  delta    sigma   weight residual
    1.513  1.460  0.053 3.90e-02 6.57e+02 1.86e+00
  bond pdb=" CB  GLU C 974 "
       pdb=" CG  GLU C 974 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.66e+00
  bond pdb=" C   PRO C 364 "
       pdb=" N   THR C 365 "
    ideal  model  delta    sigma   weight residual
    1.327  1.347 -0.020 1.71e-02 3.42e+03 1.40e+00
  ... (remaining 11125 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 15828
        2.39 -     4.79: 155
        4.79 -     7.18: 24
        7.18 -     9.57: 2
        9.57 -    11.96: 5
  Bond angle restraints: 16014
  Sorted by residual:
  angle pdb=" CA  PRO C 366 "
        pdb=" N   PRO C 366 "
        pdb=" CD  PRO C 366 "
      ideal   model   delta    sigma   weight residual
     112.00  104.01    7.99 1.40e+00 5.10e-01 3.26e+01
  angle pdb=" CB  MET C 428 "
        pdb=" CG  MET C 428 "
        pdb=" SD  MET C 428 "
      ideal   model   delta    sigma   weight residual
     112.70  124.66  -11.96 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" C3'   C E 267 "
        pdb=" O3'   C E 267 "
        pdb=" P     C E 268 "
      ideal   model   delta    sigma   weight residual
     120.20  125.96   -5.76 1.50e+00 4.44e-01 1.47e+01
  angle pdb=" C   SER C 469 "
        pdb=" N   ILE C 470 "
        pdb=" CA  ILE C 470 "
      ideal   model   delta    sigma   weight residual
     120.33  123.31   -2.98 8.00e-01 1.56e+00 1.39e+01
  angle pdb=" CA  PRO C 915 "
        pdb=" N   PRO C 915 "
        pdb=" CD  PRO C 915 "
      ideal   model   delta    sigma   weight residual
     112.00  106.78    5.22 1.40e+00 5.10e-01 1.39e+01
  ... (remaining 16009 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.45: 6257
       35.45 -    70.90: 663
       70.90 -   106.35: 71
      106.35 -   141.80: 6
      141.80 -   177.25: 3
  Dihedral angle restraints: 7000
    sinusoidal: 4726
      harmonic: 2274
  Sorted by residual:
  dihedral pdb=" O4'   C E 145 "
           pdb=" C1'   C E 145 "
           pdb=" N1    C E 145 "
           pdb=" C2    C E 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.25 -177.25     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" C4'   U E 101 "
           pdb=" C3'   U E 101 "
           pdb=" O3'   U E 101 "
           pdb=" P     G E 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   29.63 -169.63     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" O4'   G E 110 "
           pdb=" C1'   G E 110 "
           pdb=" N9    G E 110 "
           pdb=" C4    G E 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -163.81   57.81     1      1.70e+01 3.46e-03 1.55e+01
  ... (remaining 6997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1651
       0.046 -    0.091: 225
       0.091 -    0.137: 57
       0.137 -    0.183: 6
       0.183 -    0.229: 3
  Chirality restraints: 1942
  Sorted by residual:
  chirality pdb=" C1'   A E  56 "
            pdb=" O4'   A E  56 "
            pdb=" C2'   A E  56 "
            pdb=" N9    A E  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.23    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" P     C E 268 "
            pdb=" OP1   C E 268 "
            pdb=" OP2   C E 268 "
            pdb=" O5'   C E 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.62   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" C3'   U E 114 "
            pdb=" C4'   U E 114 "
            pdb=" O3'   U E 114 "
            pdb=" C2'   U E 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.56   -0.19 2.00e-01 2.50e+01 8.99e-01
  ... (remaining 1939 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 365 "   -0.056 5.00e-02 4.00e+02   8.11e-02 1.05e+01
        pdb=" N   PRO C 366 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO C 366 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C 366 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E  78 "    0.031 2.00e-02 2.50e+03   1.97e-02 8.77e+00
        pdb=" N1    C E  78 "   -0.030 2.00e-02 2.50e+03
        pdb=" C2    C E  78 "    0.023 2.00e-02 2.50e+03
        pdb=" O2    C E  78 "   -0.018 2.00e-02 2.50e+03
        pdb=" N3    C E  78 "   -0.011 2.00e-02 2.50e+03
        pdb=" C4    C E  78 "    0.019 2.00e-02 2.50e+03
        pdb=" N4    C E  78 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    C E  78 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    C E  78 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 914 "   -0.047 5.00e-02 4.00e+02   6.93e-02 7.69e+00
        pdb=" N   PRO C 915 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO C 915 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 915 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 909
        2.73 -     3.27: 10255
        3.27 -     3.81: 18936
        3.81 -     4.36: 21763
        4.36 -     4.90: 33231
  Nonbonded interactions: 85094
  Sorted by model distance:
  nonbonded pdb=" O2'   G E 112 "
            pdb=" O4'   A E 113 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O   LEU C 878 "
            pdb=" OG  SER C 881 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O2    U E 136 "
            pdb=" N2    G E 152 "
     model   vdw
     2.207 2.496
  nonbonded pdb=" NZ  LYS C 389 "
            pdb=" O   PRO C 390 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" N2    G E  33 "
            pdb=" OP2   A E  36 "
     model   vdw
     2.233 3.120
  ... (remaining 85089 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.470
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.124  11134  Z= 0.140
  Angle     :  0.622  11.963  16017  Z= 0.319
  Chirality :  0.035   0.229   1942
  Planarity :  0.005   0.081   1316
  Dihedral  : 23.522 177.250   5532
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.56 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 25.52 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.31), residues: 789
  helix:  1.47 (0.28), residues: 371
  sheet: -2.02 (0.62), residues: 63
  loop : -1.11 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 316 
 TYR   0.015   0.001   TYR C 703 
 PHE   0.025   0.002   PHE C 555 
 TRP   0.031   0.002   TRP C 388 
 HIS   0.010   0.001   HIS C 955 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (11130)
  covalent geometry    : angle       0.62208 (16014)
  hydrogen bonds       : bond        0.14845 (  444)
  hydrogen bonds       : angle       5.74314 ( 1133)
  metal coordination   : bond        0.00546 (    4)
  metal coordination   : angle       0.50472 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  309 LYS cc_start: 0.7331 (mtmm) cc_final: 0.6763 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1244
  time to fit residues: 13.2123
Evaluate side-chains
  77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:   30.0000
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
C 476 HIS
C 659 ASN
** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.177110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.116419 restraints weight = 22183.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 3.01
r_work: 0.3415 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.0760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  11134  Z= 0.132
  Angle     :  0.579  10.165  16017  Z= 0.290
  Chirality :  0.035   0.223   1942
  Planarity :  0.005   0.043   1316
  Dihedral  : 24.224 177.648   3993
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.18 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 22.09 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.31), residues: 789
  helix:  1.50 (0.28), residues: 388
  sheet: -1.76 (0.63), residues: 64
  loop : -1.06 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 316 
 TYR   0.012   0.001   TYR C1070 
 PHE   0.009   0.001   PHE C 749 
 TRP   0.016   0.001   TRP C 388 
 HIS   0.008   0.001   HIS C 955 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (11130)
  covalent geometry    : angle       0.57872 (16014)
  hydrogen bonds       : bond        0.05089 (  444)
  hydrogen bonds       : angle       4.38713 ( 1133)
  metal coordination   : bond        0.00310 (    4)
  metal coordination   : angle       1.18824 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: C  309 LYS cc_start: 0.7328 (mtmm) cc_final: 0.6971 (mtmm)
REVERT: C  446 ARG cc_start: 0.7863 (ptp-110) cc_final: 0.7175 (ptp-110)
REVERT: C  618 MET cc_start: 0.8137 (tmm) cc_final: 0.7929 (tmm)
REVERT: C  868 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.8092 (m90)
REVERT: C 1105 MET cc_start: 0.8105 (ppp) cc_final: 0.7837 (ppp)
  outliers start: 18
  outliers final: 5
  residues processed: 98
  average time/residue: 0.1334
  time to fit residues: 17.4493
Evaluate side-chains
  75 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  497 ILE
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  648 ASP
Chi-restraints excluded: chain C residue  776 GLN
Chi-restraints excluded: chain C residue  868 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 15 optimal weight:   30.0000
   chunk 87 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0980
   chunk 23 optimal weight:    0.0770
   chunk 49 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.2142

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

Flipped N/Q/H residues before XYZ refinement:
C 476 HIS
C 598 ASN
** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 769 GLN
C 955 HIS
** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.177074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.118111 restraints weight = 22002.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.97
r_work: 0.3420 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11134  Z= 0.110
  Angle     :  0.555  10.186  16017  Z= 0.277
  Chirality :  0.035   0.216   1942
  Planarity :  0.004   0.048   1316
  Dihedral  : 24.138 177.495   3993
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.30 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.09 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.31), residues: 789
  helix:  1.60 (0.28), residues: 388
  sheet: -1.74 (0.63), residues: 64
  loop : -1.05 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 316 
 TYR   0.009   0.001   TYR C 563 
 PHE   0.007   0.001   PHE C 864 
 TRP   0.020   0.001   TRP C 388 
 HIS   0.007   0.001   HIS C 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (11130)
  covalent geometry    : angle       0.55495 (16014)
  hydrogen bonds       : bond        0.04838 (  444)
  hydrogen bonds       : angle       4.08484 ( 1133)
  metal coordination   : bond        0.00680 (    4)
  metal coordination   : angle       0.92734 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: C  309 LYS cc_start: 0.7336 (mtmm) cc_final: 0.6895 (mtmm)
REVERT: C  446 ARG cc_start: 0.7942 (ptp-110) cc_final: 0.7315 (ptp-110)
REVERT: C  563 TYR cc_start: 0.7620 (m-80) cc_final: 0.7392 (m-80)
REVERT: C  868 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8151 (m90)
REVERT: C 1025 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8470 (mm-30)
REVERT: C 1105 MET cc_start: 0.8112 (ppp) cc_final: 0.7538 (ppp)
  outliers start: 20
  outliers final: 9
  residues processed: 99
  average time/residue: 0.1327
  time to fit residues: 17.6627
Evaluate side-chains
  86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  648 ASP
Chi-restraints excluded: chain C residue  681 THR
Chi-restraints excluded: chain C residue  709 GLU
Chi-restraints excluded: chain C residue  776 GLN
Chi-restraints excluded: chain C residue  868 HIS
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1037 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   chunk 74 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
C 476 HIS
C 659 ASN
C1016 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.172459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.110512 restraints weight = 22167.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.98
r_work: 0.3323 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084  11134  Z= 0.247
  Angle     :  0.672  10.080  16017  Z= 0.339
  Chirality :  0.039   0.229   1942
  Planarity :  0.005   0.049   1316
  Dihedral  : 24.374 177.282   3993
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.83 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 21.64 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.31), residues: 789
  helix:  1.26 (0.27), residues: 383
  sheet: -2.34 (0.55), residues: 69
  loop : -1.14 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 611 
 TYR   0.012   0.002   TYR C 563 
 PHE   0.014   0.002   PHE C 597 
 TRP   0.021   0.002   TRP C 388 
 HIS   0.011   0.002   HIS C 962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 (11130)
  covalent geometry    : angle       0.67114 (16014)
  hydrogen bonds       : bond        0.05717 (  444)
  hydrogen bonds       : angle       4.30408 ( 1133)
  metal coordination   : bond        0.00394 (    4)
  metal coordination   : angle       1.93667 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.296 
Fit side-chains
REVERT: C  703 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6272 (m-80)
REVERT: C  994 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8204 (mmmt)
REVERT: C 1105 MET cc_start: 0.8297 (ppp) cc_final: 0.7684 (ppp)
  outliers start: 30
  outliers final: 18
  residues processed: 103
  average time/residue: 0.1222
  time to fit residues: 17.1746
Evaluate side-chains
  88 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  497 ILE
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  621 VAL
Chi-restraints excluded: chain C residue  648 ASP
Chi-restraints excluded: chain C residue  681 THR
Chi-restraints excluded: chain C residue  703 TYR
Chi-restraints excluded: chain C residue  709 GLU
Chi-restraints excluded: chain C residue  746 ILE
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  899 THR
Chi-restraints excluded: chain C residue  976 ASN
Chi-restraints excluded: chain C residue  997 ILE
Chi-restraints excluded: chain C residue 1002 ASP
Chi-restraints excluded: chain C residue 1017 ARG
Chi-restraints excluded: chain C residue 1037 VAL
Chi-restraints excluded: chain C residue 1084 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 14 optimal weight:   30.0000
   chunk 62 optimal weight:    0.0070
   chunk 92 optimal weight:    0.0980
   chunk 2 optimal weight:   20.0000
   chunk 96 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 13 optimal weight:   40.0000
   chunk 39 optimal weight:   10.0000
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.6202

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

Flipped N/Q/H residues before XYZ refinement:
C 476 HIS
** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 868 HIS
** C 955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.174918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.113109 restraints weight = 21779.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.77
r_work: 0.3394 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11134  Z= 0.122
  Angle     :  0.584  10.282  16017  Z= 0.290
  Chirality :  0.035   0.244   1942
  Planarity :  0.004   0.052   1316
  Dihedral  : 24.285 177.412   3993
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.55 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 22.69 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.31), residues: 789
  helix:  1.54 (0.28), residues: 383
  sheet: -2.19 (0.57), residues: 69
  loop : -1.07 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C1017 
 TYR   0.013   0.001   TYR C 563 
 PHE   0.011   0.001   PHE C 864 
 TRP   0.024   0.001   TRP C 388 
 HIS   0.004   0.001   HIS C1023 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (11130)
  covalent geometry    : angle       0.58354 (16014)
  hydrogen bonds       : bond        0.05006 (  444)
  hydrogen bonds       : angle       4.04604 ( 1133)
  metal coordination   : bond        0.00790 (    4)
  metal coordination   : angle       1.25737 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.289 
Fit side-chains
REVERT: C  309 LYS cc_start: 0.7393 (mtmm) cc_final: 0.6918 (mtmm)
REVERT: C  395 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7487 (pm20)
REVERT: C  455 ARG cc_start: 0.8099 (tpm170) cc_final: 0.7680 (mmm160)
REVERT: C  576 MET cc_start: 0.7952 (tpp) cc_final: 0.7026 (tpp)
REVERT: C  618 MET cc_start: 0.7937 (tmm) cc_final: 0.7622 (tmm)
REVERT: C  963 ASN cc_start: 0.8539 (t0) cc_final: 0.8268 (t0)
REVERT: C  983 GLU cc_start: 0.8784 (tp30) cc_final: 0.8573 (tp30)
REVERT: C  994 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7998 (mmmt)
REVERT: C 1105 MET cc_start: 0.8224 (ppp) cc_final: 0.7538 (ppp)
  outliers start: 24
  outliers final: 16
  residues processed: 101
  average time/residue: 0.1292
  time to fit residues: 17.5764
Evaluate side-chains
  88 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  395 GLU
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  621 VAL
Chi-restraints excluded: chain C residue  648 ASP
Chi-restraints excluded: chain C residue  681 THR
Chi-restraints excluded: chain C residue  709 GLU
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  976 ASN
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1017 ARG
Chi-restraints excluded: chain C residue 1037 VAL
Chi-restraints excluded: chain C residue 1050 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   chunk 36 optimal weight:   30.0000
   chunk 37 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 66 optimal weight:    0.4980
   chunk 28 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9980
   chunk 32 optimal weight:   10.0000
   overall best weight:    3.8986

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

Flipped N/Q/H residues before XYZ refinement:
C 476 HIS
** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C1016 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.171842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.109961 restraints weight = 22100.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.90
r_work: 0.3327 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11134  Z= 0.208
  Angle     :  0.633  10.187  16017  Z= 0.317
  Chirality :  0.038   0.247   1942
  Planarity :  0.005   0.052   1316
  Dihedral  : 24.374 177.412   3993
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.45 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 21.64 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.31), residues: 789
  helix:  1.38 (0.28), residues: 382
  sheet: -2.40 (0.56), residues: 69
  loop : -1.14 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 611 
 TYR   0.012   0.001   TYR C 563 
 PHE   0.014   0.002   PHE C 429 
 TRP   0.023   0.002   TRP C 388 
 HIS   0.009   0.001   HIS C 962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (11130)
  covalent geometry    : angle       0.63249 (16014)
  hydrogen bonds       : bond        0.05589 (  444)
  hydrogen bonds       : angle       4.15526 ( 1133)
  metal coordination   : bond        0.00413 (    4)
  metal coordination   : angle       1.70911 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 70
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: C  388 TRP cc_start: 0.7224 (m-10) cc_final: 0.6798 (m-10)
REVERT: C  395 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7597 (pm20)
REVERT: C  618 MET cc_start: 0.7875 (tmm) cc_final: 0.7550 (tmm)
REVERT: C  703 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.5974 (m-80)
REVERT: C  868 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.8416 (m90)
REVERT: C  994 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8008 (mmmt)
REVERT: C 1105 MET cc_start: 0.8336 (ppp) cc_final: 0.7508 (ppp)
  outliers start: 36
  outliers final: 20
  residues processed: 99
  average time/residue: 0.1195
  time to fit residues: 16.5291
Evaluate side-chains
  93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  346 GLU
Chi-restraints excluded: chain C residue  395 GLU
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  513 LEU
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  621 VAL
Chi-restraints excluded: chain C residue  648 ASP
Chi-restraints excluded: chain C residue  681 THR
Chi-restraints excluded: chain C residue  703 TYR
Chi-restraints excluded: chain C residue  709 GLU
Chi-restraints excluded: chain C residue  746 ILE
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  802 SER
Chi-restraints excluded: chain C residue  868 HIS
Chi-restraints excluded: chain C residue  947 ILE
Chi-restraints excluded: chain C residue  976 ASN
Chi-restraints excluded: chain C residue  997 ILE
Chi-restraints excluded: chain C residue 1037 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 13 optimal weight:   40.0000
   chunk 22 optimal weight:   20.0000
   chunk 47 optimal weight:    3.9990
   chunk 15 optimal weight:   30.0000
   chunk 19 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 4 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9980
   chunk 55 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9990
   chunk 14 optimal weight:   20.0000
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.172520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.110975 restraints weight = 21940.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.84
r_work: 0.3347 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11134  Z= 0.173
  Angle     :  0.629  12.529  16017  Z= 0.311
  Chirality :  0.037   0.254   1942
  Planarity :  0.005   0.052   1316
  Dihedral  : 24.386 177.430   3993
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.44 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 23.58 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.31), residues: 789
  helix:  1.40 (0.27), residues: 382
  sheet: -2.35 (0.55), residues: 69
  loop : -1.16 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 455 
 TYR   0.010   0.001   TYR C 563 
 PHE   0.015   0.002   PHE C 429 
 TRP   0.022   0.002   TRP C 388 
 HIS   0.005   0.001   HIS C 962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (11130)
  covalent geometry    : angle       0.62822 (16014)
  hydrogen bonds       : bond        0.05504 (  444)
  hydrogen bonds       : angle       4.10137 ( 1133)
  metal coordination   : bond        0.00483 (    4)
  metal coordination   : angle       1.58167 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: C  309 LYS cc_start: 0.7338 (mtmm) cc_final: 0.6867 (mtmm)
REVERT: C  388 TRP cc_start: 0.7246 (m-10) cc_final: 0.7021 (m-10)
REVERT: C  395 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7577 (pm20)
REVERT: C  618 MET cc_start: 0.7910 (tmm) cc_final: 0.7589 (tmm)
REVERT: C  703 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5756 (m-80)
REVERT: C  868 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8380 (m90)
REVERT: C  994 LYS cc_start: 0.8322 (mmmt) cc_final: 0.7983 (mmmt)
REVERT: C 1101 ARG cc_start: 0.7604 (tpt170) cc_final: 0.7378 (tpt170)
REVERT: C 1105 MET cc_start: 0.8267 (ppp) cc_final: 0.7415 (ppp)
  outliers start: 26
  outliers final: 18
  residues processed: 94
  average time/residue: 0.1226
  time to fit residues: 15.9065
Evaluate side-chains
  86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  346 GLU
Chi-restraints excluded: chain C residue  395 GLU
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  513 LEU
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  621 VAL
Chi-restraints excluded: chain C residue  648 ASP
Chi-restraints excluded: chain C residue  681 THR
Chi-restraints excluded: chain C residue  703 TYR
Chi-restraints excluded: chain C residue  709 GLU
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  802 SER
Chi-restraints excluded: chain C residue  868 HIS
Chi-restraints excluded: chain C residue  947 ILE
Chi-restraints excluded: chain C residue  976 ASN
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1037 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 55 optimal weight:   20.0000
   chunk 61 optimal weight:    0.7980
   chunk 44 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
C 598 ASN
C 955 HIS
** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.174433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.113169 restraints weight = 22080.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.76
r_work: 0.3391 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11134  Z= 0.120
  Angle     :  0.588  10.840  16017  Z= 0.291
  Chirality :  0.036   0.233   1942
  Planarity :  0.004   0.052   1316
  Dihedral  : 24.326 177.468   3993
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.44 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.73 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.31), residues: 789
  helix:  1.65 (0.28), residues: 376
  sheet: -2.22 (0.55), residues: 69
  loop : -1.11 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 455 
 TYR   0.010   0.001   TYR C 563 
 PHE   0.014   0.001   PHE C 429 
 TRP   0.021   0.001   TRP C 388 
 HIS   0.006   0.001   HIS C 962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (11130)
  covalent geometry    : angle       0.58770 (16014)
  hydrogen bonds       : bond        0.05342 (  444)
  hydrogen bonds       : angle       3.91746 ( 1133)
  metal coordination   : bond        0.00964 (    4)
  metal coordination   : angle       1.43670 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: C  395 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7531 (pm20)
REVERT: C  572 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7521 (p)
REVERT: C  618 MET cc_start: 0.7877 (tmm) cc_final: 0.7556 (tmm)
REVERT: C  868 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.8189 (m90)
REVERT: C  994 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7820 (mmmt)
REVERT: C 1105 MET cc_start: 0.8249 (ppp) cc_final: 0.7339 (ppp)
  outliers start: 22
  outliers final: 18
  residues processed: 89
  average time/residue: 0.1170
  time to fit residues: 14.6041
Evaluate side-chains
  88 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  346 GLU
Chi-restraints excluded: chain C residue  395 GLU
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  648 ASP
Chi-restraints excluded: chain C residue  681 THR
Chi-restraints excluded: chain C residue  709 GLU
Chi-restraints excluded: chain C residue  746 ILE
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  802 SER
Chi-restraints excluded: chain C residue  868 HIS
Chi-restraints excluded: chain C residue  951 CYS
Chi-restraints excluded: chain C residue  976 ASN
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1016 GLN
Chi-restraints excluded: chain C residue 1037 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 29 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 92 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 15 optimal weight:   30.0000
   chunk 59 optimal weight:    1.9990
   chunk 17 optimal weight:   40.0000
   chunk 58 optimal weight:    8.9990
   chunk 66 optimal weight:    0.2980
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
C 963 ASN
** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.173509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.112425 restraints weight = 22131.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.82
r_work: 0.3370 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11134  Z= 0.146
  Angle     :  0.604  10.690  16017  Z= 0.300
  Chirality :  0.036   0.229   1942
  Planarity :  0.005   0.051   1316
  Dihedral  : 24.319 177.510   3993
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.18 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 23.73 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.31), residues: 789
  helix:  1.58 (0.28), residues: 383
  sheet: -2.19 (0.55), residues: 69
  loop : -1.15 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 455 
 TYR   0.009   0.001   TYR C 628 
 PHE   0.016   0.002   PHE C 429 
 TRP   0.049   0.002   TRP C 388 
 HIS   0.006   0.001   HIS C 955 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (11130)
  covalent geometry    : angle       0.60384 (16014)
  hydrogen bonds       : bond        0.05544 (  444)
  hydrogen bonds       : angle       3.98305 ( 1133)
  metal coordination   : bond        0.00706 (    4)
  metal coordination   : angle       1.24570 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  388 TRP cc_start: 0.7288 (m-10) cc_final: 0.6823 (m-10)
REVERT: C  395 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7687 (pt0)
REVERT: C  572 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7548 (p)
REVERT: C  618 MET cc_start: 0.7870 (tmm) cc_final: 0.7537 (tmm)
REVERT: C  703 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6336 (m-80)
REVERT: C  868 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.8277 (m90)
REVERT: C  994 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7851 (mmmt)
REVERT: C 1105 MET cc_start: 0.8283 (ppp) cc_final: 0.7447 (ppp)
  outliers start: 23
  outliers final: 19
  residues processed: 93
  average time/residue: 0.1204
  time to fit residues: 15.5125
Evaluate side-chains
  93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  346 GLU
Chi-restraints excluded: chain C residue  395 GLU
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  621 VAL
Chi-restraints excluded: chain C residue  648 ASP
Chi-restraints excluded: chain C residue  681 THR
Chi-restraints excluded: chain C residue  703 TYR
Chi-restraints excluded: chain C residue  709 GLU
Chi-restraints excluded: chain C residue  746 ILE
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  802 SER
Chi-restraints excluded: chain C residue  868 HIS
Chi-restraints excluded: chain C residue  951 CYS
Chi-restraints excluded: chain C residue  976 ASN
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1016 GLN
Chi-restraints excluded: chain C residue 1037 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 24 optimal weight:   20.0000
   chunk 77 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0060
   chunk 64 optimal weight:    0.9990
   chunk 4 optimal weight:   30.0000
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:   30.0000
   chunk 97 optimal weight:    9.9990
   chunk 23 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0970
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.177092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.116626 restraints weight = 21822.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.68
r_work: 0.3452 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11134  Z= 0.105
  Angle     :  0.590  12.391  16017  Z= 0.290
  Chirality :  0.035   0.207   1942
  Planarity :  0.004   0.052   1316
  Dihedral  : 24.235 177.468   3993
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.42 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 24.18 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.31), residues: 789
  helix:  1.75 (0.28), residues: 376
  sheet: -1.96 (0.56), residues: 69
  loop : -1.10 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 455 
 TYR   0.009   0.001   TYR C1070 
 PHE   0.014   0.001   PHE C 429 
 TRP   0.030   0.001   TRP C 388 
 HIS   0.004   0.001   HIS C 955 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (11130)
  covalent geometry    : angle       0.58924 (16014)
  hydrogen bonds       : bond        0.05418 (  444)
  hydrogen bonds       : angle       3.87347 ( 1133)
  metal coordination   : bond        0.01211 (    4)
  metal coordination   : angle       1.48933 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: C  395 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7545 (pm20)
REVERT: C  572 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7484 (p)
REVERT: C  618 MET cc_start: 0.7797 (tmm) cc_final: 0.7430 (tmm)
REVERT: C  868 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.8167 (m90)
REVERT: C  983 GLU cc_start: 0.8789 (tp30) cc_final: 0.8544 (tp30)
REVERT: C  994 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7732 (mmmt)
REVERT: C 1105 MET cc_start: 0.8145 (ppp) cc_final: 0.7311 (ppp)
  outliers start: 21
  outliers final: 16
  residues processed: 96
  average time/residue: 0.1085
  time to fit residues: 14.6586
Evaluate side-chains
  91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  346 GLU
Chi-restraints excluded: chain C residue  395 GLU
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  648 ASP
Chi-restraints excluded: chain C residue  681 THR
Chi-restraints excluded: chain C residue  709 GLU
Chi-restraints excluded: chain C residue  802 SER
Chi-restraints excluded: chain C residue  868 HIS
Chi-restraints excluded: chain C residue  951 CYS
Chi-restraints excluded: chain C residue  976 ASN
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1016 GLN
Chi-restraints excluded: chain C residue 1037 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 90 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0370
   chunk 16 optimal weight:   30.0000
   chunk 81 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   overall best weight:    3.8066

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

Flipped N/Q/H residues before XYZ refinement:
C 718 HIS
C 963 ASN
** C1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1032 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.172807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.112333 restraints weight = 22333.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.95
r_work: 0.3332 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11134  Z= 0.210
  Angle     :  0.654  10.031  16017  Z= 0.328
  Chirality :  0.038   0.211   1942
  Planarity :  0.005   0.051   1316
  Dihedral  : 24.340 177.686   3993
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.32 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 24.48 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.31), residues: 789
  helix:  1.49 (0.27), residues: 383
  sheet: -2.22 (0.56), residues: 69
  loop : -1.21 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 455 
 TYR   0.010   0.002   TYR C 789 
 PHE   0.020   0.002   PHE C 429 
 TRP   0.045   0.002   TRP C 388 
 HIS   0.007   0.001   HIS C 962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (11130)
  covalent geometry    : angle       0.65339 (16014)
  hydrogen bonds       : bond        0.06165 (  444)
  hydrogen bonds       : angle       4.16949 ( 1133)
  metal coordination   : bond        0.00454 (    4)
  metal coordination   : angle       1.58241 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3396.47 seconds
wall clock time: 58 minutes 47.81 seconds (3527.81 seconds total)