Starting phenix.real_space_refine
on Wed Mar  4 09:36:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v5c_21052/03_2026/6v5c_21052.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v5c_21052/03_2026/6v5c_21052.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/6v5c_21052/03_2026/6v5c_21052.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v5c_21052/03_2026/6v5c_21052.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v5c_21052/03_2026/6v5c_21052.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v5c_21052/03_2026/6v5c_21052.cif"
  }
  resolution = 4.4
  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=   0.007 sd=   0.091
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      66      5.49       5
     S      69      5.16       5
     C    7523      2.51       5
     N    2158      2.21       5
     O    2435      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12251
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 903, 7371
          Classifications: {'peptide': 903}
          Link IDs: {'PTRANS': 49, 'TRANS': 853}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1747
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 208}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1739
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 8, 'TRANS': 207}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 1394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 1394
          Classifications: {'RNA': 66}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 29, 'rna3p_pyr': 35}
          Link IDs: {'rna2p': 2, 'rna3p': 63}
          Chain breaks: 1
  Time building chain proxies: 3.02, per 1000 atoms: 0.25
  Number of scatterers: 12251
  At special positions: 0
  Unit cell: (97.52, 114.48, 169.6, 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      69     16.00
     P      66     15.00
     O    2435      8.00
     N    2158      7.00
     C    7523      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: 0.99
  Conformation dependent library (CDL) restraints added in 546.5 milliseconds
  

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2530

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 9 sheets defined
      42.9% alpha, 6.1% beta
      27 base pairs and 39 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 442 through 447
      removed outlier: 3.573A  pdb=" N   TYR A 445 " --> pdb=" O   ARG A 442 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASP A 446 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS A 447 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 442 through 447'
    Processing helix  chain 'A' and resid 504 through 512
      removed outlier: 3.849A  pdb=" N   LYS A 512 " --> pdb=" O   ILE A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 538
      removed outlier: 4.470A  pdb=" N   GLY A 533 " --> pdb=" O   MET A 530 " (cutoff:3.500A)
      Proline residue:  A 534  - end of helix
    Processing helix  chain 'A' and resid 642 through 654
    Processing helix  chain 'A' and resid 698 through 708
    Processing helix  chain 'A' and resid 726 through 737
    Processing helix  chain 'A' and resid 777 through 781
      removed outlier: 4.343A  pdb=" N   ALA A 780 " --> pdb=" O   ILE A 777 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLN A 781 " --> pdb=" O   ARG A 778 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 777 through 781'
    Processing helix  chain 'A' and resid 782 through 786
    Processing helix  chain 'A' and resid 787 through 804
    Processing helix  chain 'A' and resid 812 through 830
      removed outlier: 3.932A  pdb=" N   GLN A 816 " --> pdb=" O   GLN A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 875
      removed outlier: 4.157A  pdb=" N   HIS A 868 " --> pdb=" O   PRO A 864 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   CYS A 875 " --> pdb=" O   ARG A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 882
      removed outlier: 3.544A  pdb=" N   ASP A 880 " --> pdb=" O   MET A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 897
    Processing helix  chain 'A' and resid 909 through 920
    Processing helix  chain 'A' and resid 965 through 986
      removed outlier: 3.984A  pdb=" N   LEU A 971 " --> pdb=" O   ARG A 967 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ALA A 974 " --> pdb=" O   PHE A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1004
    Processing helix  chain 'A' and resid 1005 through 1017
    Processing helix  chain 'A' and resid 1033 through 1055
    Processing helix  chain 'A' and resid 1056 through 1063
      removed outlier: 3.998A  pdb=" N   ALA A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1064 through 1069
    Processing helix  chain 'A' and resid 1071 through 1080
    Processing helix  chain 'A' and resid 1084 through 1089
      removed outlier: 3.522A  pdb=" N   GLN A1089 " --> pdb=" O   PRO A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1103 through 1115
      removed outlier: 4.062A  pdb=" N   LEU A1107 " --> pdb=" O   VAL A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1127
      removed outlier: 4.368A  pdb=" N   LEU A1124 " --> pdb=" O   HIS A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1165
      removed outlier: 4.444A  pdb=" N   LEU A1149 " --> pdb=" O   ARG A1145 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR A1159 " --> pdb=" O   GLN A1155 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ILE A1164 " --> pdb=" O   GLU A1160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1182
    Processing helix  chain 'A' and resid 1185 through 1195
    Processing helix  chain 'A' and resid 1214 through 1226
    Processing helix  chain 'A' and resid 1234 through 1245
      removed outlier: 3.589A  pdb=" N   HIS A1238 " --> pdb=" O   LEU A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1255
    Processing helix  chain 'A' and resid 1260 through 1269
      removed outlier: 3.737A  pdb=" N   GLN A1264 " --> pdb=" O   ASP A1260 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS A1269 " --> pdb=" O   LEU A1265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1303 through 1307
      removed outlier: 3.690A  pdb=" N   GLY A1306 " --> pdb=" O   TYR A1303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1317 through 1332
      removed outlier: 3.753A  pdb=" N   GLU A1321 " --> pdb=" O   ILE A1317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1345
      removed outlier: 4.188A  pdb=" N   ILE A1344 " --> pdb=" O   GLN A1340 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU A1345 " --> pdb=" O   LYS A1341 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1340 through 1345'
    Processing helix  chain 'C' and resid 511 through 523
    Processing helix  chain 'C' and resid 561 through 575
      removed outlier: 3.881A  pdb=" N   LYS C 565 " --> pdb=" O   LYS C 561 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 612 through 616
      removed outlier: 4.393A  pdb=" N   ALA C 615 " --> pdb=" O   THR C 612 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY C 616 " --> pdb=" O   SER C 613 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 612 through 616'
    Processing helix  chain 'C' and resid 618 through 631
      removed outlier: 3.661A  pdb=" N   LEU C 624 " --> pdb=" O   PRO C 620 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 668 through 685
    Processing helix  chain 'C' and resid 693 through 698
    Processing helix  chain 'C' and resid 729 through 750
    Processing helix  chain 'B' and resid 511 through 523
      removed outlier: 3.939A  pdb=" N   ILE B 515 " --> pdb=" O   SER B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 576
    Processing helix  chain 'B' and resid 597 through 601
      removed outlier: 4.098A  pdb=" N   HIS B 600 " --> pdb=" O   TYR B 597 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 613
      removed outlier: 3.556A  pdb=" N   THR B 612 " --> pdb=" O   TYR B 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 627
    Processing helix  chain 'B' and resid 668 through 685
      removed outlier: 3.958A  pdb=" N   GLY B 672 " --> pdb=" O   ASN B 668 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   HIS B 685 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 692 through 698
    Processing helix  chain 'B' and resid 730 through 748
    Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415
      removed outlier: 6.691A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 572 through 573
    Processing sheet with id=AA3, first strand: chain 'A' and resid 572 through 573
      removed outlier: 4.529A  pdb=" N   ARG A 684 " --> pdb=" O   GLU A 602 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   PHE A 604 " --> pdb=" O   MET A 682 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   MET A 682 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 618 through 621
      removed outlier: 3.664A  pdb=" N   CYS A 618 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 740 through 741
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1289 through 1290
    Processing sheet with id=AA7, first strand: chain 'C' and resid 530 through 534
      removed outlier: 3.564A  pdb=" N   ASN C 531 " --> pdb=" O   SER C 545 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   SER C 545 " --> pdb=" O   ASN C 531 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE C 533 " --> pdb=" O   GLY C 543 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   VAL C 546 " --> pdb=" O   TYR C 553 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 639 through 641
    Processing sheet with id=AA9, first strand: chain 'B' and resid 529 through 533
      removed outlier: 4.047A  pdb=" N   GLY B 554 " --> pdb=" O   VAL B 546 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ILE B 548 " --> pdb=" O   THR B 552 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   THR B 552 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1098 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      65 hydrogen bonds
      122 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      39 stacking parallelities
  Total time for adding SS restraints: 1.93

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1944
        1.32 -     1.45: 3905
        1.45 -     1.58: 6565
        1.58 -     1.72: 133
        1.72 -     1.85: 108
  Bond restraints: 12655
  Sorted by residual:
  bond pdb=" CA  ASN A 963 "
       pdb=" C   ASN A 963 "
    ideal  model  delta    sigma   weight residual
    1.525  1.430  0.095 1.27e-02 6.20e+03 5.63e+01
  bond pdb=" CA  TYR C 609 "
       pdb=" C   TYR C 609 "
    ideal  model  delta    sigma   weight residual
    1.523  1.600 -0.076 1.34e-02 5.57e+03 3.24e+01
  bond pdb=" CA  VAL C 608 "
       pdb=" C   VAL C 608 "
    ideal  model  delta    sigma   weight residual
    1.520  1.587 -0.067 1.20e-02 6.94e+03 3.14e+01
  bond pdb=" N   TYR C 621 "
       pdb=" CA  TYR C 621 "
    ideal  model  delta    sigma   weight residual
    1.459  1.392  0.067 1.20e-02 6.94e+03 3.13e+01
  bond pdb=" CA  TRP A1258 "
       pdb=" C   TRP A1258 "
    ideal  model  delta    sigma   weight residual
    1.530  1.471  0.059 1.17e-02 7.31e+03 2.57e+01
  ... (remaining 12650 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.61: 17020
        3.61 -     7.22: 292
        7.22 -    10.83: 47
       10.83 -    14.44: 12
       14.44 -    18.04: 8
  Bond angle restraints: 17379
  Sorted by residual:
  angle pdb=" N   VAL C 608 "
        pdb=" CA  VAL C 608 "
        pdb=" C   VAL C 608 "
      ideal   model   delta    sigma   weight residual
     113.47  130.83  -17.36 1.01e+00 9.80e-01 2.95e+02
  angle pdb=" CA  GLU A 736 "
        pdb=" C   GLU A 736 "
        pdb=" N   CYS A 737 "
      ideal   model   delta    sigma   weight residual
     117.72  103.02   14.70 1.31e+00 5.83e-01 1.26e+02
  angle pdb=" C   THR A 958 "
        pdb=" N   PRO A 959 "
        pdb=" CA  PRO A 959 "
      ideal   model   delta    sigma   weight residual
     119.84  106.39   13.45 1.25e+00 6.40e-01 1.16e+02
  angle pdb=" N   TRP A1258 "
        pdb=" CA  TRP A1258 "
        pdb=" C   TRP A1258 "
      ideal   model   delta    sigma   weight residual
     111.28   97.25   14.03 1.35e+00 5.49e-01 1.08e+02
  angle pdb=" N   GLU C 604 "
        pdb=" CA  GLU C 604 "
        pdb=" C   GLU C 604 "
      ideal   model   delta    sigma   weight residual
     113.01  125.43  -12.42 1.20e+00 6.94e-01 1.07e+02
  ... (remaining 17374 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.29: 6535
       18.29 -    36.58: 870
       36.58 -    54.87: 222
       54.87 -    73.16: 124
       73.16 -    91.46: 22
  Dihedral angle restraints: 7773
    sinusoidal: 3870
      harmonic: 3903
  Sorted by residual:
  dihedral pdb=" CA  ASN B 668 "
           pdb=" C   ASN B 668 "
           pdb=" N   LYS B 669 "
           pdb=" CA  LYS B 669 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.52  -36.48     0      5.00e+00 4.00e-02 5.32e+01
  dihedral pdb=" CA  VAL A 773 "
           pdb=" C   VAL A 773 "
           pdb=" N   HIS A 774 "
           pdb=" CA  HIS A 774 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.62   35.38     0      5.00e+00 4.00e-02 5.01e+01
  dihedral pdb=" CA  HIS A 983 "
           pdb=" C   HIS A 983 "
           pdb=" N   LEU A 984 "
           pdb=" CA  LEU A 984 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.50   33.50     0      5.00e+00 4.00e-02 4.49e+01
  ... (remaining 7770 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.128: 1845
       0.128 -    0.257: 84
       0.257 -    0.385: 5
       0.385 -    0.514: 5
       0.514 -    0.642: 4
  Chirality restraints: 1943
  Sorted by residual:
  chirality pdb=" CA  VAL C 608 "
            pdb=" N   VAL C 608 "
            pdb=" C   VAL C 608 "
            pdb=" CB  VAL C 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.80    0.64 2.00e-01 2.50e+01 1.03e+01
  chirality pdb=" CA  TYR C 621 "
            pdb=" N   TYR C 621 "
            pdb=" C   TYR C 621 "
            pdb=" CB  TYR C 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.87    0.64 2.00e-01 2.50e+01 1.03e+01
  chirality pdb=" CA  GLU C 604 "
            pdb=" N   GLU C 604 "
            pdb=" C   GLU C 604 "
            pdb=" CB  GLU C 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.59 2.00e-01 2.50e+01 8.61e+00
  ... (remaining 1940 not shown)

  Planarity restraints: 1998
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 736 "   -0.017 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   GLU A 736 "    0.071 2.00e-02 2.50e+03
        pdb=" O   GLU A 736 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   CYS A 737 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1258 "   -0.043 2.00e-02 2.50e+03   2.23e-02 1.24e+01
        pdb=" CG  TRP A1258 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1258 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1258 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1258 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1258 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1258 "    0.043 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1258 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1258 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1258 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 514 "   -0.056 5.00e-02 4.00e+02   8.53e-02 1.17e+01
        pdb=" N   PRO A 515 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A 515 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 515 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 1995 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 238
        2.60 -     3.17: 10110
        3.17 -     3.75: 21409
        3.75 -     4.32: 26159
        4.32 -     4.90: 38977
  Nonbonded interactions: 96893
  Sorted by model distance:
  nonbonded pdb=" O   MET A 740 "
            pdb=" CZ  PHE A 847 "
     model   vdw
     2.023 3.340
  nonbonded pdb=" O   PHE A1252 "
            pdb=" ND2 ASN A1255 "
     model   vdw
     2.038 3.120
  nonbonded pdb=" CE  MET A 740 "
            pdb=" CB  CYS A 920 "
     model   vdw
     2.105 3.860
  nonbonded pdb=" OG  SER C 613 "
            pdb=" CB  SER C 619 "
     model   vdw
     2.185 3.440
  nonbonded pdb=" OE2 GLU C 594 "
            pdb=" NH2 ARG C 696 "
     model   vdw
     2.239 3.120
  ... (remaining 96888 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 'B' and (resid 493 through 495 or (resid 496 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 500 through 749))
  selection = (chain 'C' and resid 493 through 749)
}

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:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.500
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.095  12655  Z= 0.400
  Angle     :  1.265  18.044  17379  Z= 0.723
  Chirality :  0.071   0.642   1943
  Planarity :  0.008   0.085   1998
  Dihedral  : 19.090  91.456   5243
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 13.72 %
    Favored  : 85.90 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.82 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.55 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    Twisted General : 0.64 %

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 are not related in a simple way.
  whole: -4.86 (0.19), residues: 1312
  helix: -2.35 (0.19), residues: 502
  sheet: -3.03 (0.50), residues: 61
  loop : -4.08 (0.19), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 548 
 TYR   0.050   0.003   TYR C 621 
 PHE   0.024   0.003   PHE A 631 
 TRP   0.043   0.003   TRP A1258 
 HIS   0.011   0.002   HIS A 573 

Details of bonding type rmsd
  covalent geometry    : bond        0.00694 (12655)
  covalent geometry    : angle       1.26506 (17379)
  hydrogen bonds       : bond        0.16366 (  449)
  hydrogen bonds       : angle       7.95975 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  699 MET cc_start: 0.8229 (tpp) cc_final: 0.7596 (tpt)
REVERT: A  784 TYR cc_start: 0.7424 (m-10) cc_final: 0.7058 (m-80)
REVERT: A  861 MET cc_start: 0.9215 (mpp) cc_final: 0.8689 (mpp)
REVERT: A  897 MET cc_start: 0.8434 (ttp) cc_final: 0.8215 (ttp)
REVERT: A 1011 MET cc_start: 0.8934 (mmm) cc_final: 0.8657 (tpp)
REVERT: A 1014 LYS cc_start: 0.9689 (tptm) cc_final: 0.9434 (tppt)
REVERT: A 1022 MET cc_start: 0.8525 (ptm) cc_final: 0.8177 (ptp)
REVERT: A 1026 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.7809 (t70)
REVERT: A 1043 CYS cc_start: 0.8906 (p) cc_final: 0.8673 (p)
REVERT: A 1151 ASP cc_start: 0.8645 (p0) cc_final: 0.8376 (p0)
REVERT: A 1235 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9083 (tp30)
REVERT: A 1241 MET cc_start: 0.9166 (mmm) cc_final: 0.8901 (mmt)
REVERT: C  501 LYS cc_start: 0.6871 (ptmm) cc_final: 0.5667 (mttt)
REVERT: C  520 MET cc_start: 0.8558 (mtp) cc_final: 0.8009 (ttt)
REVERT: C  609 TYR cc_start: 0.1694 (OUTLIER) cc_final: 0.0350 (m-80)
REVERT: B  682 GLN cc_start: 0.8821 (mm110) cc_final: 0.8351 (mt0)
REVERT: B  697 MET cc_start: 0.9302 (mtp) cc_final: 0.9032 (mmm)
  outliers start: 22
  outliers final: 11
  residues processed: 151
  average time/residue: 0.0973
  time to fit residues: 21.9167
Evaluate side-chains
  108 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 964 HIS
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1136 ASN
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 521 GLN
B 625 HIS
B 660 HIS
** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.055580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.042602 restraints weight = 95437.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.043963 restraints weight = 58592.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.044896 restraints weight = 41959.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.045520 restraints weight = 33160.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.045951 restraints weight = 28100.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  12655  Z= 0.247
  Angle     :  0.818  11.726  17379  Z= 0.422
  Chirality :  0.046   0.239   1943
  Planarity :  0.007   0.070   1998
  Dihedral  : 17.792  87.533   2469
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 18.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 14.10 %
    Favored  : 85.82 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  8.63 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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 are not related in a simple way.
  whole: -3.90 (0.21), residues: 1312
  helix: -1.12 (0.21), residues: 524
  sheet: -2.71 (0.58), residues: 51
  loop : -3.93 (0.19), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 548 
 TYR   0.028   0.002   TYR A 872 
 PHE   0.017   0.003   PHE B 641 
 TRP   0.018   0.002   TRP B 665 
 HIS   0.011   0.002   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 (12655)
  covalent geometry    : angle       0.81803 (17379)
  hydrogen bonds       : bond        0.05499 (  449)
  hydrogen bonds       : angle       6.12695 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 114
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  562 ARG cc_start: 0.7467 (tpp-160) cc_final: 0.7106 (tpp80)
REVERT: A  722 MET cc_start: 0.8900 (tmm) cc_final: 0.8618 (tmm)
REVERT: A  740 MET cc_start: 0.8537 (mtp) cc_final: 0.7866 (tpt)
REVERT: A  897 MET cc_start: 0.8476 (ttp) cc_final: 0.8009 (ttp)
REVERT: A 1011 MET cc_start: 0.9082 (mmm) cc_final: 0.8667 (tpp)
REVERT: A 1235 GLU cc_start: 0.9519 (mt-10) cc_final: 0.9140 (mm-30)
REVERT: A 1241 MET cc_start: 0.9328 (mmm) cc_final: 0.8977 (mmt)
REVERT: A 1322 MET cc_start: 0.9046 (ttt) cc_final: 0.8779 (ttt)
REVERT: C  494 VAL cc_start: 0.6894 (m) cc_final: 0.6241 (t)
REVERT: C  501 LYS cc_start: 0.6507 (ptmm) cc_final: 0.5379 (mmtm)
REVERT: C  520 MET cc_start: 0.8433 (mtp) cc_final: 0.7919 (mmm)
REVERT: C  697 MET cc_start: 0.7819 (ptt) cc_final: 0.7412 (ptt)
REVERT: B  682 GLN cc_start: 0.8916 (mm110) cc_final: 0.8539 (mt0)
  outliers start: 3
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1055
  time to fit residues: 18.4170
Evaluate side-chains
  94 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 80 optimal weight:    0.4980
   chunk 32 optimal weight:    5.9990
   chunk 81 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   chunk 12 optimal weight:    8.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 924 GLN
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1294 HIS
** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 678 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.058453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.045756 restraints weight = 94572.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.047154 restraints weight = 58872.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.048090 restraints weight = 42187.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.048737 restraints weight = 33372.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.049175 restraints weight = 28195.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12655  Z= 0.139
  Angle     :  0.704  11.887  17379  Z= 0.357
  Chirality :  0.042   0.204   1943
  Planarity :  0.005   0.068   1998
  Dihedral  : 17.452  86.896   2469
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.96 %
    Favored  : 87.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -3.33 (0.22), residues: 1312
  helix: -0.44 (0.23), residues: 510
  sheet: -2.23 (0.59), residues: 56
  loop : -3.74 (0.20), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1000 
 TYR   0.034   0.002   TYR A 872 
 PHE   0.016   0.002   PHE A1343 
 TRP   0.030   0.002   TRP A 725 
 HIS   0.006   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (12655)
  covalent geometry    : angle       0.70365 (17379)
  hydrogen bonds       : bond        0.04591 (  449)
  hydrogen bonds       : angle       5.59162 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  562 ARG cc_start: 0.7284 (tpp-160) cc_final: 0.6983 (tpp80)
REVERT: A  722 MET cc_start: 0.8795 (tmm) cc_final: 0.8502 (tmm)
REVERT: A  897 MET cc_start: 0.7935 (ttp) cc_final: 0.7723 (ttp)
REVERT: A 1011 MET cc_start: 0.9026 (mmm) cc_final: 0.8770 (tpp)
REVERT: A 1146 MET cc_start: 0.8725 (mpp) cc_final: 0.8445 (mpp)
REVERT: A 1235 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9055 (mm-30)
REVERT: A 1241 MET cc_start: 0.9366 (mmm) cc_final: 0.8985 (mmt)
REVERT: A 1258 TRP cc_start: 0.8106 (t60) cc_final: 0.7869 (t-100)
REVERT: A 1322 MET cc_start: 0.9014 (ttt) cc_final: 0.8683 (ttt)
REVERT: C  501 LYS cc_start: 0.6617 (ptmm) cc_final: 0.5982 (mmtm)
REVERT: C  520 MET cc_start: 0.8381 (mtp) cc_final: 0.8002 (ttm)
REVERT: C  697 MET cc_start: 0.7828 (ptt) cc_final: 0.7425 (ptt)
REVERT: B  520 MET cc_start: 0.8934 (ttp) cc_final: 0.8457 (ppp)
REVERT: B  521 GLN cc_start: 0.9398 (mm110) cc_final: 0.8715 (tm-30)
REVERT: B  697 MET cc_start: 0.8644 (mmm) cc_final: 0.8318 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0911
  time to fit residues: 17.6251
Evaluate side-chains
  97 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0670
   chunk 107 optimal weight:   30.0000
   chunk 70 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   chunk 75 optimal weight:    2.9990
   chunk 110 optimal weight:   20.0000
   chunk 50 optimal weight:    0.8980
   overall best weight:    3.1924

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 934 HIS
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.056852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.044048 restraints weight = 95201.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.045406 restraints weight = 59586.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.046321 restraints weight = 42964.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.046959 restraints weight = 34143.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.047325 restraints weight = 28986.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12655  Z= 0.177
  Angle     :  0.725  11.578  17379  Z= 0.368
  Chirality :  0.043   0.185   1943
  Planarity :  0.005   0.069   1998
  Dihedral  : 17.433  85.437   2469
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.48 %
    Favored  : 85.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -3.16 (0.22), residues: 1312
  helix: -0.32 (0.23), residues: 516
  sheet: -2.02 (0.66), residues: 47
  loop : -3.64 (0.20), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1000 
 TYR   0.043   0.002   TYR A 872 
 PHE   0.015   0.002   PHE B 641 
 TRP   0.016   0.002   TRP A 725 
 HIS   0.007   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (12655)
  covalent geometry    : angle       0.72485 (17379)
  hydrogen bonds       : bond        0.04714 (  449)
  hydrogen bonds       : angle       5.43486 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  699 MET cc_start: 0.8980 (mmp) cc_final: 0.8700 (mmp)
REVERT: A  722 MET cc_start: 0.8896 (tmm) cc_final: 0.8626 (tmm)
REVERT: A  740 MET cc_start: 0.8508 (tpp) cc_final: 0.8143 (tpp)
REVERT: A  897 MET cc_start: 0.8365 (ttp) cc_final: 0.7901 (ttp)
REVERT: A  920 CYS cc_start: 0.8193 (p) cc_final: 0.7865 (p)
REVERT: A 1011 MET cc_start: 0.9048 (mmm) cc_final: 0.8794 (tpp)
REVERT: A 1022 MET cc_start: 0.8663 (ptp) cc_final: 0.8276 (ptp)
REVERT: A 1040 MET cc_start: 0.9034 (mmt) cc_final: 0.8673 (mmt)
REVERT: A 1241 MET cc_start: 0.9399 (mmm) cc_final: 0.9020 (mmt)
REVERT: A 1308 ARG cc_start: 0.7694 (ptt180) cc_final: 0.7288 (ppt170)
REVERT: A 1322 MET cc_start: 0.9034 (ttt) cc_final: 0.8753 (ttt)
REVERT: C  501 LYS cc_start: 0.6106 (ptmm) cc_final: 0.5612 (mmtm)
REVERT: C  514 CYS cc_start: 0.9605 (m) cc_final: 0.9398 (m)
REVERT: C  520 MET cc_start: 0.8243 (mtp) cc_final: 0.7813 (ttm)
REVERT: C  697 MET cc_start: 0.7900 (ptt) cc_final: 0.7535 (ptt)
REVERT: B  521 GLN cc_start: 0.9461 (mm110) cc_final: 0.7996 (tm-30)
REVERT: B  682 GLN cc_start: 0.8928 (mm110) cc_final: 0.8623 (mt0)
REVERT: B  697 MET cc_start: 0.8614 (mmm) cc_final: 0.8286 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0984
  time to fit residues: 16.3962
Evaluate side-chains
  90 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 93 optimal weight:    9.9990
   chunk 121 optimal weight:    9.9990
   chunk 125 optimal weight:    0.1980
   chunk 39 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 116 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   overall best weight:    3.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 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 = 0.3425 r_free = 0.3425 target = 0.056658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.043670 restraints weight = 96915.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.045098 restraints weight = 58908.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.046056 restraints weight = 41805.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.046703 restraints weight = 32803.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.047153 restraints weight = 27732.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  12655  Z= 0.198
  Angle     :  0.743  13.955  17379  Z= 0.376
  Chirality :  0.044   0.267   1943
  Planarity :  0.005   0.068   1998
  Dihedral  : 17.489  85.604   2469
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.48 %
    Favored  : 85.52 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.19 %
    Favored  : 95.73 %
  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 are not related in a simple way.
  whole: -3.09 (0.22), residues: 1312
  helix: -0.32 (0.23), residues: 523
  sheet: -2.01 (0.60), residues: 57
  loop : -3.60 (0.20), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1000 
 TYR   0.048   0.002   TYR A 872 
 PHE   0.014   0.002   PHE A 653 
 TRP   0.014   0.001   TRP A 725 
 HIS   0.008   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (12655)
  covalent geometry    : angle       0.74264 (17379)
  hydrogen bonds       : bond        0.04759 (  449)
  hydrogen bonds       : angle       5.44446 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  699 MET cc_start: 0.8997 (mmp) cc_final: 0.8554 (mmp)
REVERT: A  722 MET cc_start: 0.8925 (tmm) cc_final: 0.8607 (tmm)
REVERT: A  848 TRP cc_start: 0.7899 (m-90) cc_final: 0.7526 (m-90)
REVERT: A  897 MET cc_start: 0.8240 (ttp) cc_final: 0.7883 (ttp)
REVERT: A  937 MET cc_start: 0.4329 (mpp) cc_final: 0.3888 (mpp)
REVERT: A 1011 MET cc_start: 0.9086 (mmm) cc_final: 0.8843 (tpp)
REVERT: A 1022 MET cc_start: 0.8766 (ptp) cc_final: 0.8496 (ptp)
REVERT: A 1040 MET cc_start: 0.9088 (mmt) cc_final: 0.8749 (mmt)
REVERT: A 1146 MET cc_start: 0.8885 (mpp) cc_final: 0.8463 (mpp)
REVERT: A 1241 MET cc_start: 0.9411 (mmm) cc_final: 0.9052 (mmt)
REVERT: A 1308 ARG cc_start: 0.7617 (ptt180) cc_final: 0.7210 (ptt180)
REVERT: A 1322 MET cc_start: 0.9053 (ttt) cc_final: 0.8808 (ttt)
REVERT: C  501 LYS cc_start: 0.6404 (ptmm) cc_final: 0.5688 (mmtm)
REVERT: C  514 CYS cc_start: 0.9617 (m) cc_final: 0.9416 (m)
REVERT: C  520 MET cc_start: 0.8344 (mtp) cc_final: 0.8001 (ttp)
REVERT: C  697 MET cc_start: 0.7942 (ptt) cc_final: 0.7576 (ptt)
REVERT: B  520 MET cc_start: 0.9031 (ttp) cc_final: 0.8522 (ppp)
REVERT: B  521 GLN cc_start: 0.9464 (mm110) cc_final: 0.8630 (tm-30)
REVERT: B  682 GLN cc_start: 0.8976 (mm110) cc_final: 0.8698 (mt0)
REVERT: B  697 MET cc_start: 0.8680 (mmm) cc_final: 0.8399 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0983
  time to fit residues: 16.8689
Evaluate side-chains
  89 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 132 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   chunk 116 optimal weight:    9.9990
   chunk 7 optimal weight:    9.9990
   chunk 135 optimal weight:   10.0000
   chunk 122 optimal weight:    0.0980
   chunk 101 optimal weight:   10.0000
   chunk 128 optimal weight:    5.9990
   overall best weight:    3.2188

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

Flipped N/Q/H residues before XYZ refinement:
** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 632 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.056853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.044054 restraints weight = 96200.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.045411 restraints weight = 60309.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.046315 restraints weight = 43540.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.046956 restraints weight = 34730.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.047382 restraints weight = 29488.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12655  Z= 0.173
  Angle     :  0.710  11.519  17379  Z= 0.361
  Chirality :  0.044   0.198   1943
  Planarity :  0.005   0.067   1998
  Dihedral  : 17.422  84.454   2469
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 14.63 %
    Favored  : 85.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  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 are not related in a simple way.
  whole: -2.99 (0.22), residues: 1312
  helix: -0.21 (0.23), residues: 522
  sheet: -1.66 (0.63), residues: 57
  loop : -3.58 (0.20), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 548 
 TYR   0.050   0.002   TYR A 872 
 PHE   0.013   0.002   PHE B 641 
 TRP   0.013   0.001   TRP A 725 
 HIS   0.007   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (12655)
  covalent geometry    : angle       0.70978 (17379)
  hydrogen bonds       : bond        0.04562 (  449)
  hydrogen bonds       : angle       5.28604 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  722 MET cc_start: 0.8687 (tmm) cc_final: 0.8470 (tmm)
REVERT: A  937 MET cc_start: 0.4047 (mpp) cc_final: 0.3580 (mpp)
REVERT: A 1011 MET cc_start: 0.9058 (mmm) cc_final: 0.8810 (tpp)
REVERT: A 1022 MET cc_start: 0.8682 (ptp) cc_final: 0.8442 (ptp)
REVERT: A 1040 MET cc_start: 0.8970 (mmt) cc_final: 0.8521 (mmt)
REVERT: A 1241 MET cc_start: 0.9424 (mmm) cc_final: 0.9006 (mmt)
REVERT: A 1322 MET cc_start: 0.9025 (ttt) cc_final: 0.8808 (ttt)
REVERT: C  501 LYS cc_start: 0.7043 (pptt) cc_final: 0.6522 (mmtm)
REVERT: C  520 MET cc_start: 0.8374 (mtp) cc_final: 0.7889 (mmm)
REVERT: C  697 MET cc_start: 0.7833 (ptt) cc_final: 0.7493 (ptt)
REVERT: B  682 GLN cc_start: 0.8900 (mm110) cc_final: 0.8663 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0914
  time to fit residues: 15.5227
Evaluate side-chains
  83 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 127 optimal weight:    8.9990
   chunk 117 optimal weight:    6.9990
   chunk 98 optimal weight:    0.3980
   chunk 87 optimal weight:    8.9990
   chunk 95 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 35 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    3.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 521 GLN
B 632 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.056568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.043656 restraints weight = 95116.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.045102 restraints weight = 57511.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.046065 restraints weight = 40722.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.046732 restraints weight = 32068.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.047187 restraints weight = 26995.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12655  Z= 0.183
  Angle     :  0.727  11.767  17379  Z= 0.369
  Chirality :  0.044   0.250   1943
  Planarity :  0.005   0.067   1998
  Dihedral  : 17.409  83.058   2469
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.71 %
    Favored  : 85.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  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 are not related in a simple way.
  whole: -2.91 (0.22), residues: 1312
  helix: -0.16 (0.23), residues: 520
  sheet: -1.52 (0.68), residues: 52
  loop : -3.51 (0.21), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 548 
 TYR   0.056   0.002   TYR A 872 
 PHE   0.037   0.002   PHE A 970 
 TRP   0.014   0.001   TRP B 665 
 HIS   0.007   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (12655)
  covalent geometry    : angle       0.72696 (17379)
  hydrogen bonds       : bond        0.04657 (  449)
  hydrogen bonds       : angle       5.31303 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  618 CYS cc_start: 0.8604 (t) cc_final: 0.8356 (t)
REVERT: A  699 MET cc_start: 0.9070 (mmp) cc_final: 0.8489 (mmp)
REVERT: A  722 MET cc_start: 0.8691 (tmm) cc_final: 0.8472 (tmm)
REVERT: A  848 TRP cc_start: 0.7874 (m-90) cc_final: 0.7570 (m-90)
REVERT: A  937 MET cc_start: 0.4003 (mpp) cc_final: 0.3165 (mtt)
REVERT: A 1011 MET cc_start: 0.9098 (mmm) cc_final: 0.8873 (tpp)
REVERT: A 1040 MET cc_start: 0.9035 (mmt) cc_final: 0.8259 (mmt)
REVERT: A 1146 MET cc_start: 0.8870 (mpp) cc_final: 0.8482 (mpp)
REVERT: A 1235 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9254 (mm-30)
REVERT: A 1241 MET cc_start: 0.9465 (mmm) cc_final: 0.9084 (mmt)
REVERT: A 1308 ARG cc_start: 0.7574 (ptt180) cc_final: 0.6774 (ptt180)
REVERT: A 1322 MET cc_start: 0.9023 (ttt) cc_final: 0.8783 (ttt)
REVERT: C  501 LYS cc_start: 0.7240 (pptt) cc_final: 0.6857 (mmtm)
REVERT: C  520 MET cc_start: 0.8274 (mtp) cc_final: 0.7702 (mmm)
REVERT: C  697 MET cc_start: 0.7893 (ptt) cc_final: 0.7552 (ptt)
REVERT: B  520 MET cc_start: 0.9054 (ttp) cc_final: 0.8284 (ppp)
REVERT: B  521 GLN cc_start: 0.9434 (mm110) cc_final: 0.8371 (tm-30)
REVERT: B  682 GLN cc_start: 0.8969 (mm110) cc_final: 0.8692 (mt0)
REVERT: B  697 MET cc_start: 0.8544 (mmm) cc_final: 0.8258 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0901
  time to fit residues: 15.8223
Evaluate side-chains
  89 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 128 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 119 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 116 optimal weight:   10.0000
   chunk 133 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0980
   chunk 91 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    2.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1080 ASN
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.056982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.044323 restraints weight = 94944.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.045685 restraints weight = 59347.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.046595 restraints weight = 42913.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.047217 restraints weight = 34234.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.047603 restraints weight = 29152.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12655  Z= 0.157
  Angle     :  0.724  11.926  17379  Z= 0.364
  Chirality :  0.043   0.204   1943
  Planarity :  0.005   0.067   1998
  Dihedral  : 17.273  81.673   2469
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.80 %
    Favored  : 86.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  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 are not related in a simple way.
  whole: -2.81 (0.23), residues: 1312
  helix: -0.05 (0.23), residues: 520
  sheet: -1.35 (0.69), residues: 52
  loop : -3.49 (0.21), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 548 
 TYR   0.054   0.002   TYR A 872 
 PHE   0.032   0.002   PHE A 970 
 TRP   0.018   0.002   TRP C 665 
 HIS   0.006   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (12655)
  covalent geometry    : angle       0.72439 (17379)
  hydrogen bonds       : bond        0.04438 (  449)
  hydrogen bonds       : angle       5.19172 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  618 CYS cc_start: 0.8510 (t) cc_final: 0.8249 (t)
REVERT: A  699 MET cc_start: 0.9059 (mmp) cc_final: 0.8664 (mmp)
REVERT: A  848 TRP cc_start: 0.7833 (m-90) cc_final: 0.7514 (m-90)
REVERT: A  937 MET cc_start: 0.4385 (mpp) cc_final: 0.3522 (mtt)
REVERT: A 1011 MET cc_start: 0.9038 (mmm) cc_final: 0.8806 (tpp)
REVERT: A 1022 MET cc_start: 0.8518 (ptp) cc_final: 0.8092 (ptp)
REVERT: A 1040 MET cc_start: 0.9148 (mmt) cc_final: 0.8519 (mmt)
REVERT: A 1235 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9228 (mm-30)
REVERT: A 1241 MET cc_start: 0.9434 (mmm) cc_final: 0.9003 (mmt)
REVERT: A 1308 ARG cc_start: 0.7593 (ptt180) cc_final: 0.6853 (ptt180)
REVERT: A 1322 MET cc_start: 0.8995 (ttt) cc_final: 0.8763 (ttt)
REVERT: C  501 LYS cc_start: 0.7344 (pptt) cc_final: 0.7021 (mmtm)
REVERT: C  520 MET cc_start: 0.8361 (mtp) cc_final: 0.7870 (mmm)
REVERT: C  697 MET cc_start: 0.7787 (ptt) cc_final: 0.7457 (ptt)
REVERT: B  520 MET cc_start: 0.9109 (ttp) cc_final: 0.8352 (ppp)
REVERT: B  521 GLN cc_start: 0.9410 (mm110) cc_final: 0.8408 (tm-30)
REVERT: B  682 GLN cc_start: 0.8934 (mm110) cc_final: 0.8669 (mt0)
REVERT: B  697 MET cc_start: 0.8508 (mmm) cc_final: 0.8146 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0898
  time to fit residues: 15.5749
Evaluate side-chains
  90 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 111 optimal weight:   30.0000
   chunk 118 optimal weight:    9.9990
   chunk 136 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 88 optimal weight:    0.9990
   chunk 67 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 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 = 0.3448 r_free = 0.3448 target = 0.057909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.045641 restraints weight = 101452.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.047006 restraints weight = 62761.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.047920 restraints weight = 44952.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.048542 restraints weight = 35641.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.048959 restraints weight = 30251.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12655  Z= 0.180
  Angle     :  0.732  11.780  17379  Z= 0.371
  Chirality :  0.044   0.199   1943
  Planarity :  0.005   0.067   1998
  Dihedral  : 17.252  79.944   2469
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.48 %
    Favored  : 85.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.22), residues: 1312
  helix:  0.01 (0.23), residues: 513
  sheet: -1.57 (0.66), residues: 57
  loop : -3.54 (0.21), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 548 
 TYR   0.059   0.002   TYR A 872 
 PHE   0.028   0.002   PHE A 970 
 TRP   0.013   0.001   TRP B 665 
 HIS   0.007   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (12655)
  covalent geometry    : angle       0.73213 (17379)
  hydrogen bonds       : bond        0.04573 (  449)
  hydrogen bonds       : angle       5.24208 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  618 CYS cc_start: 0.8377 (t) cc_final: 0.8118 (t)
REVERT: A  699 MET cc_start: 0.9113 (mmp) cc_final: 0.8596 (mmp)
REVERT: A  848 TRP cc_start: 0.7667 (m-90) cc_final: 0.7374 (m-90)
REVERT: A  862 MET cc_start: 0.8890 (mmm) cc_final: 0.8629 (mmm)
REVERT: A  937 MET cc_start: 0.4450 (mpp) cc_final: 0.3593 (mtt)
REVERT: A 1011 MET cc_start: 0.9016 (mmm) cc_final: 0.8765 (tpp)
REVERT: A 1022 MET cc_start: 0.8494 (ptp) cc_final: 0.8239 (ptp)
REVERT: A 1040 MET cc_start: 0.9047 (mmt) cc_final: 0.8660 (mmt)
REVERT: A 1146 MET cc_start: 0.8861 (mpp) cc_final: 0.8511 (mpp)
REVERT: A 1241 MET cc_start: 0.9438 (mmm) cc_final: 0.9011 (mmt)
REVERT: A 1322 MET cc_start: 0.9028 (ttt) cc_final: 0.8801 (ttt)
REVERT: C  501 LYS cc_start: 0.7358 (pptt) cc_final: 0.6949 (mmtm)
REVERT: C  514 CYS cc_start: 0.9490 (m) cc_final: 0.9276 (m)
REVERT: C  520 MET cc_start: 0.8386 (mtp) cc_final: 0.7924 (mmm)
REVERT: C  697 MET cc_start: 0.7842 (ptt) cc_final: 0.7539 (ptt)
REVERT: B  520 MET cc_start: 0.9192 (ttp) cc_final: 0.8450 (ppp)
REVERT: B  521 GLN cc_start: 0.9424 (mm110) cc_final: 0.8496 (tm-30)
REVERT: B  682 GLN cc_start: 0.8980 (mm110) cc_final: 0.8749 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0934
  time to fit residues: 15.9380
Evaluate side-chains
  91 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 76 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0270
   chunk 45 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 94 optimal weight:   40.0000
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.8042

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

Flipped N/Q/H residues before XYZ refinement:
A 663 ASN
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1173 HIS
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 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 = 0.3463 r_free = 0.3463 target = 0.058149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.045567 restraints weight = 94781.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.046941 restraints weight = 59471.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.047883 restraints weight = 42803.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.048536 restraints weight = 33791.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.048991 restraints weight = 28516.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  12655  Z= 0.132
  Angle     :  0.704  12.264  17379  Z= 0.350
  Chirality :  0.043   0.191   1943
  Planarity :  0.005   0.067   1998
  Dihedral  : 16.950  76.833   2469
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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 are not related in a simple way.
  whole: -2.68 (0.23), residues: 1312
  helix:  0.11 (0.23), residues: 526
  sheet: -1.37 (0.67), residues: 57
  loop : -3.49 (0.21), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1000 
 TYR   0.045   0.002   TYR A 872 
 PHE   0.022   0.001   PHE A 970 
 TRP   0.014   0.001   TRP B 665 
 HIS   0.006   0.001   HIS A 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (12655)
  covalent geometry    : angle       0.70423 (17379)
  hydrogen bonds       : bond        0.04170 (  449)
  hydrogen bonds       : angle       5.04574 ( 1220)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  618 CYS cc_start: 0.8387 (t) cc_final: 0.8070 (t)
REVERT: A  636 MET cc_start: 0.8157 (mmt) cc_final: 0.7726 (tpp)
REVERT: A  699 MET cc_start: 0.9088 (mmp) cc_final: 0.8625 (mmp)
REVERT: A  848 TRP cc_start: 0.7677 (m-90) cc_final: 0.7316 (m-90)
REVERT: A  862 MET cc_start: 0.8946 (mmm) cc_final: 0.8614 (mmm)
REVERT: A  937 MET cc_start: 0.4375 (mpp) cc_final: 0.3355 (mtt)
REVERT: A 1011 MET cc_start: 0.8995 (mmm) cc_final: 0.8765 (tpp)
REVERT: A 1022 MET cc_start: 0.8601 (ptp) cc_final: 0.8289 (ptp)
REVERT: A 1146 MET cc_start: 0.8781 (mpp) cc_final: 0.8354 (mpp)
REVERT: A 1241 MET cc_start: 0.9426 (mmm) cc_final: 0.9033 (mmt)
REVERT: A 1308 ARG cc_start: 0.7653 (ptt180) cc_final: 0.7121 (ptt180)
REVERT: A 1322 MET cc_start: 0.8956 (ttt) cc_final: 0.8709 (ttt)
REVERT: C  514 CYS cc_start: 0.9465 (m) cc_final: 0.9244 (m)
REVERT: C  520 MET cc_start: 0.8473 (mtp) cc_final: 0.8002 (mmm)
REVERT: C  697 MET cc_start: 0.7905 (ptt) cc_final: 0.7615 (ptt)
REVERT: B  521 GLN cc_start: 0.9152 (mm110) cc_final: 0.8547 (tm-30)
REVERT: B  682 GLN cc_start: 0.8918 (mm110) cc_final: 0.8647 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0943
  time to fit residues: 16.8647
Evaluate side-chains
  88 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 131 optimal weight:    9.9990
   chunk 106 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 110 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 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 = 0.3429 r_free = 0.3429 target = 0.056914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.044405 restraints weight = 96567.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.045700 restraints weight = 61355.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.046604 restraints weight = 44764.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.047221 restraints weight = 35748.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.047633 restraints weight = 30457.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.4114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12655  Z= 0.180
  Angle     :  0.727  11.934  17379  Z= 0.368
  Chirality :  0.044   0.188   1943
  Planarity :  0.005   0.067   1998
  Dihedral  : 17.001  77.980   2469
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.33 %
    Favored  : 85.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  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 are not related in a simple way.
  whole: -2.79 (0.22), residues: 1312
  helix: -0.03 (0.23), residues: 527
  sheet: -1.34 (0.67), residues: 57
  loop : -3.53 (0.21), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 548 
 TYR   0.059   0.002   TYR A 872 
 PHE   0.020   0.002   PHE A 970 
 TRP   0.012   0.001   TRP B 665 
 HIS   0.009   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12655)
  covalent geometry    : angle       0.72679 (17379)
  hydrogen bonds       : bond        0.04589 (  449)
  hydrogen bonds       : angle       5.18431 ( 1220)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1887.79 seconds
wall clock time: 33 minutes 44.73 seconds (2024.73 seconds total)