Starting phenix.real_space_refine
on Wed Jul 30 16:59:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v5c_21052/07_2025/6v5c_21052.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v5c_21052/07_2025/6v5c_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_21052/07_2025/6v5c_21052.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v5c_21052/07_2025/6v5c_21052.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v5c_21052/07_2025/6v5c_21052.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v5c_21052/07_2025/6v5c_21052.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.26, per 1000 atoms: 0.67
  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: 3.41
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 4.98
  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: 5.37

  Time building geometry restraints manager: 3.94 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:             1.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     38.410
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.360
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.043   0.003   TRP A1258 
 HIS   0.011   0.002   HIS A 573 
 PHE   0.024   0.003   PHE A 631 
 TYR   0.050   0.003   TYR C 621 
 ARG   0.010   0.001   ARG A 548 

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

*********************** 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  : 1.593 
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: 0.8214 (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: 0.2470
  time to fit residues: 55.4047
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  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 108 optimal weight:   20.0000
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:   20.0000
   chunk 80 optimal weight:    6.9990
   chunk 125 optimal weight:   10.0000
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.3414 r_free = 0.3414 target = 0.056548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.043521 restraints weight = 93880.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.044911 restraints weight = 57711.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.045851 restraints weight = 41328.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  12655  Z= 0.208
  Angle     :  0.778  11.856  17379  Z= 0.400
  Chirality :  0.045   0.238   1943
  Planarity :  0.006   0.070   1998
  Dihedral  : 17.652  86.551   2469
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 13.19 %
    Favored  : 86.74 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.71 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.77 (0.21), residues: 1312
  helix: -1.00 (0.22), residues: 515
  sheet: -2.56 (0.60), residues: 51
  loop : -3.83 (0.19), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 665 
 HIS   0.009   0.001   HIS A1026 
 PHE   0.017   0.002   PHE B 641 
 TYR   0.027   0.002   TYR A 872 
 ARG   0.009   0.001   ARG A 548 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05193 (  449)
  hydrogen bonds       : angle       6.00310 ( 1220)
  covalent geometry    : bond        0.00433 (12655)
  covalent geometry    : angle       0.77827 (17379)

*********************** 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
  123 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  562 ARG cc_start: 0.7406 (tpp-160) cc_final: 0.7088 (tpp80)
REVERT: A  722 MET cc_start: 0.8899 (tmm) cc_final: 0.8613 (tmm)
REVERT: A  740 MET cc_start: 0.8415 (mtp) cc_final: 0.7774 (tpt)
REVERT: A  848 TRP cc_start: 0.8164 (m-90) cc_final: 0.7757 (m-90)
REVERT: A  897 MET cc_start: 0.8315 (ttp) cc_final: 0.7875 (ttp)
REVERT: A  937 MET cc_start: 0.2876 (mmt) cc_final: 0.2650 (mpp)
REVERT: A 1011 MET cc_start: 0.9054 (mmm) cc_final: 0.8629 (tpp)
REVERT: A 1235 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9090 (mm-30)
REVERT: A 1241 MET cc_start: 0.9274 (mmm) cc_final: 0.8986 (mmt)
REVERT: A 1322 MET cc_start: 0.8995 (ttt) cc_final: 0.8737 (ttt)
REVERT: C  494 VAL cc_start: 0.6809 (m) cc_final: 0.6248 (t)
REVERT: C  501 LYS cc_start: 0.6320 (ptmm) cc_final: 0.5327 (mmtm)
REVERT: C  520 MET cc_start: 0.8409 (mtp) cc_final: 0.8028 (ttm)
REVERT: C  697 MET cc_start: 0.7968 (ptt) cc_final: 0.7485 (ptt)
REVERT: B  682 GLN cc_start: 0.8914 (mm110) cc_final: 0.8505 (mt0)
  outliers start: 3
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2718
  time to fit residues: 50.1097
Evaluate side-chains
  98 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 85 optimal weight:    8.9990
   chunk 58 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0370
   chunk 10 optimal weight:    0.3980
   chunk 38 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 132 optimal weight:   10.0000
   chunk 78 optimal weight:    0.0970
   overall best weight:    1.7060

-------------------------------------------------------------------------------
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 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.058392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.045579 restraints weight = 93314.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.047078 restraints weight = 55924.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.048092 restraints weight = 39176.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12655  Z= 0.140
  Angle     :  0.703  12.422  17379  Z= 0.356
  Chirality :  0.042   0.193   1943
  Planarity :  0.005   0.069   1998
  Dihedral  : 17.408  86.112   2469
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.73 %
    Favored  : 87.27 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.22), residues: 1312
  helix: -0.45 (0.23), residues: 518
  sheet: -1.87 (0.69), residues: 45
  loop : -3.71 (0.19), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1258 
 HIS   0.007   0.001   HIS A 859 
 PHE   0.015   0.002   PHE A1343 
 TYR   0.035   0.002   TYR A 872 
 ARG   0.007   0.000   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  449)
  hydrogen bonds       : angle       5.53285 ( 1220)
  covalent geometry    : bond        0.00305 (12655)
  covalent geometry    : angle       0.70261 (17379)

*********************** 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
  128 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 2.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  697 LEU cc_start: 0.8318 (tp) cc_final: 0.7935 (mt)
REVERT: A  722 MET cc_start: 0.8891 (tmm) cc_final: 0.8637 (tmm)
REVERT: A  848 TRP cc_start: 0.8005 (m-90) cc_final: 0.7738 (m-90)
REVERT: A  897 MET cc_start: 0.8023 (ttp) cc_final: 0.7774 (ttp)
REVERT: A 1011 MET cc_start: 0.9066 (mmm) cc_final: 0.8805 (tpp)
REVERT: A 1235 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9091 (mm-30)
REVERT: A 1241 MET cc_start: 0.9393 (mmm) cc_final: 0.8968 (mmt)
REVERT: A 1322 MET cc_start: 0.8966 (ttt) cc_final: 0.8664 (ttt)
REVERT: C  501 LYS cc_start: 0.6623 (ptmm) cc_final: 0.5981 (mmtm)
REVERT: C  520 MET cc_start: 0.8385 (mtp) cc_final: 0.7993 (ttm)
REVERT: C  697 MET cc_start: 0.7899 (ptt) cc_final: 0.7510 (ptt)
REVERT: B  520 MET cc_start: 0.8936 (ttp) cc_final: 0.8467 (ppp)
REVERT: B  521 GLN cc_start: 0.9467 (mm110) cc_final: 0.8761 (tm-30)
REVERT: B  697 MET cc_start: 0.8656 (mmm) cc_final: 0.8432 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.3104
  time to fit residues: 60.4757
Evaluate side-chains
  99 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 81 optimal weight:    8.9990
   chunk 48 optimal weight:   30.0000
   chunk 96 optimal weight:   30.0000
   chunk 17 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 132 optimal weight:   10.0000
   overall best weight:    3.1986

-------------------------------------------------------------------------------
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 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 = 0.3441 r_free = 0.3441 target = 0.057291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.044592 restraints weight = 94514.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.045952 restraints weight = 59163.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.046862 restraints weight = 42708.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12655  Z= 0.179
  Angle     :  0.720  11.886  17379  Z= 0.366
  Chirality :  0.043   0.203   1943
  Planarity :  0.005   0.069   1998
  Dihedral  : 17.406  85.127   2469
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.10 %
    Favored  : 85.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.22), residues: 1312
  helix: -0.26 (0.23), residues: 514
  sheet: -1.58 (0.72), residues: 45
  loop : -3.68 (0.19), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 665 
 HIS   0.007   0.001   HIS A 983 
 PHE   0.016   0.002   PHE B 598 
 TYR   0.042   0.002   TYR A 872 
 ARG   0.008   0.001   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04665 (  449)
  hydrogen bonds       : angle       5.46761 ( 1220)
  covalent geometry    : bond        0.00378 (12655)
  covalent geometry    : angle       0.71968 (17379)

*********************** 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
  117 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.149 
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  682 MET cc_start: 0.7723 (tmm) cc_final: 0.7161 (tmm)
REVERT: A  722 MET cc_start: 0.8929 (tmm) cc_final: 0.8664 (tmm)
REVERT: A  740 MET cc_start: 0.7904 (tpp) cc_final: 0.7438 (tpp)
REVERT: A  848 TRP cc_start: 0.8035 (m-90) cc_final: 0.7742 (m-90)
REVERT: A  897 MET cc_start: 0.8363 (ttp) cc_final: 0.7909 (ttp)
REVERT: A 1011 MET cc_start: 0.9054 (mmm) cc_final: 0.8805 (tpp)
REVERT: A 1022 MET cc_start: 0.8746 (ptp) cc_final: 0.8396 (ptp)
REVERT: A 1040 MET cc_start: 0.9045 (mmt) cc_final: 0.8713 (mmt)
REVERT: A 1241 MET cc_start: 0.9402 (mmm) cc_final: 0.9027 (mmt)
REVERT: A 1308 ARG cc_start: 0.8135 (ptt180) cc_final: 0.7713 (ptt180)
REVERT: A 1322 MET cc_start: 0.9012 (ttt) cc_final: 0.8772 (ttt)
REVERT: C  501 LYS cc_start: 0.6411 (ptmm) cc_final: 0.5858 (mmtm)
REVERT: C  520 MET cc_start: 0.8245 (mtp) cc_final: 0.7780 (ttm)
REVERT: C  697 MET cc_start: 0.7882 (ptt) cc_final: 0.7511 (ptt)
REVERT: B  521 GLN cc_start: 0.9473 (mm110) cc_final: 0.8017 (tm-30)
REVERT: B  682 GLN cc_start: 0.8909 (mm110) cc_final: 0.8601 (mt0)
REVERT: B  697 MET cc_start: 0.8615 (mmm) cc_final: 0.8272 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.3781
  time to fit residues: 66.0470
Evaluate side-chains
  93 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 1.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 88 optimal weight:    8.9990
   chunk 94 optimal weight:   20.0000
   chunk 29 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0040
   chunk 69 optimal weight:    9.9990
   chunk 75 optimal weight:    0.8980
   chunk 63 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 109 optimal weight:   30.0000
   overall best weight:    1.5798

-------------------------------------------------------------------------------
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 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1042 ASN
** 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 = 0.3481 r_free = 0.3481 target = 0.058885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.046229 restraints weight = 93463.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.047621 restraints weight = 58302.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.048566 restraints weight = 41849.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  12655  Z= 0.133
  Angle     :  0.683  11.779  17379  Z= 0.342
  Chirality :  0.042   0.246   1943
  Planarity :  0.005   0.068   1998
  Dihedral  : 17.216  83.497   2469
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.96 %
    Favored  : 87.04 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.10 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.22), residues: 1312
  helix: -0.12 (0.23), residues: 521
  sheet: -1.50 (0.72), residues: 47
  loop : -3.59 (0.20), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A 725 
 HIS   0.005   0.001   HIS A 983 
 PHE   0.015   0.002   PHE B 598 
 TYR   0.038   0.001   TYR A 872 
 ARG   0.005   0.000   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04259 (  449)
  hydrogen bonds       : angle       5.22950 ( 1220)
  covalent geometry    : bond        0.00296 (12655)
  covalent geometry    : angle       0.68323 (17379)

*********************** 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
  123 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 1.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  682 MET cc_start: 0.7661 (tmm) cc_final: 0.7122 (tmm)
REVERT: A  697 LEU cc_start: 0.8308 (tp) cc_final: 0.7951 (mt)
REVERT: A  722 MET cc_start: 0.9032 (tmm) cc_final: 0.8458 (ttm)
REVERT: A  752 VAL cc_start: 0.8958 (t) cc_final: 0.8686 (t)
REVERT: A  848 TRP cc_start: 0.7989 (m-90) cc_final: 0.7641 (m-90)
REVERT: A 1011 MET cc_start: 0.9003 (mmm) cc_final: 0.8764 (tpp)
REVERT: A 1022 MET cc_start: 0.8686 (ptp) cc_final: 0.8410 (ptp)
REVERT: A 1040 MET cc_start: 0.9150 (mmt) cc_final: 0.8822 (mmt)
REVERT: A 1146 MET cc_start: 0.8790 (mpp) cc_final: 0.8426 (mpp)
REVERT: A 1241 MET cc_start: 0.9405 (mmm) cc_final: 0.8981 (mmt)
REVERT: A 1308 ARG cc_start: 0.8125 (ptt180) cc_final: 0.7691 (ptt180)
REVERT: A 1322 MET cc_start: 0.8961 (ttt) cc_final: 0.8652 (ttt)
REVERT: C  501 LYS cc_start: 0.6570 (ptmm) cc_final: 0.6228 (mmtm)
REVERT: C  505 ILE cc_start: 0.8949 (mp) cc_final: 0.8706 (mp)
REVERT: C  520 MET cc_start: 0.8315 (mtp) cc_final: 0.7963 (ttm)
REVERT: C  697 MET cc_start: 0.7813 (ptt) cc_final: 0.7486 (ptt)
REVERT: B  520 MET cc_start: 0.8977 (ttp) cc_final: 0.8460 (ppp)
REVERT: B  521 GLN cc_start: 0.9427 (mm110) cc_final: 0.8879 (tm-30)
REVERT: B  605 ASP cc_start: 0.5085 (m-30) cc_final: 0.4714 (m-30)
REVERT: B  697 MET cc_start: 0.8584 (mmm) cc_final: 0.8225 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2488
  time to fit residues: 46.6109
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  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 48 optimal weight:   30.0000
   chunk 93 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 106 optimal weight:    6.9990
   chunk 112 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1042 ASN
** 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 = 0.3395 r_free = 0.3395 target = 0.055628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.042788 restraints weight = 95082.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.044172 restraints weight = 57822.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.045103 restraints weight = 41183.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12655  Z= 0.256
  Angle     :  0.783  11.931  17379  Z= 0.403
  Chirality :  0.046   0.288   1943
  Planarity :  0.006   0.067   1998
  Dihedral  : 17.528  83.942   2469
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 20.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.47 %
    Favored  : 84.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.22), residues: 1312
  helix: -0.20 (0.23), residues: 516
  sheet: -1.41 (0.75), residues: 45
  loop : -3.61 (0.20), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 725 
 HIS   0.016   0.002   HIS A 774 
 PHE   0.020   0.002   PHE A 653 
 TYR   0.054   0.002   TYR A 872 
 ARG   0.011   0.001   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05203 (  449)
  hydrogen bonds       : angle       5.50256 ( 1220)
  covalent geometry    : bond        0.00533 (12655)
  covalent geometry    : angle       0.78326 (17379)

*********************** 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
  102 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.511 
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  682 MET cc_start: 0.8056 (tmm) cc_final: 0.7740 (tmm)
REVERT: A  722 MET cc_start: 0.8781 (tmm) cc_final: 0.8539 (tmm)
REVERT: A  848 TRP cc_start: 0.8158 (m-90) cc_final: 0.7814 (m-90)
REVERT: A  937 MET cc_start: 0.3981 (mpp) cc_final: 0.3528 (mpp)
REVERT: A 1011 MET cc_start: 0.9119 (mmm) cc_final: 0.8862 (tpp)
REVERT: A 1022 MET cc_start: 0.8713 (ptp) cc_final: 0.8417 (ptp)
REVERT: A 1040 MET cc_start: 0.8999 (mmt) cc_final: 0.8206 (mmt)
REVERT: A 1241 MET cc_start: 0.9470 (mmm) cc_final: 0.9101 (mmt)
REVERT: A 1308 ARG cc_start: 0.8080 (ptt180) cc_final: 0.7700 (ptm160)
REVERT: A 1322 MET cc_start: 0.9087 (ttt) cc_final: 0.8800 (ttt)
REVERT: C  501 LYS cc_start: 0.6701 (ptmm) cc_final: 0.6123 (mmtm)
REVERT: C  503 PHE cc_start: 0.8119 (p90) cc_final: 0.7443 (p90)
REVERT: C  514 CYS cc_start: 0.9566 (m) cc_final: 0.9360 (m)
REVERT: C  520 MET cc_start: 0.8425 (mtp) cc_final: 0.7992 (mmm)
REVERT: C  530 TYR cc_start: 0.7845 (m-80) cc_final: 0.7335 (m-80)
REVERT: C  697 MET cc_start: 0.7973 (ptt) cc_final: 0.7610 (ptt)
REVERT: B  520 MET cc_start: 0.9011 (ttp) cc_final: 0.8244 (ttp)
REVERT: B  697 MET cc_start: 0.8641 (mmm) cc_final: 0.8225 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.2248
  time to fit residues: 35.9813
Evaluate side-chains
  81 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 111 optimal weight:   30.0000
   chunk 32 optimal weight:    9.9990
   chunk 119 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 67 optimal weight:    0.3980
   chunk 126 optimal weight:    4.9990
   chunk 99 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 96 optimal weight:   20.0000
   chunk 106 optimal weight:    9.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    5.0788

-------------------------------------------------------------------------------
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 774 HIS ** 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 = 0.3397 r_free = 0.3397 target = 0.055587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.042632 restraints weight = 96761.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.044073 restraints weight = 58362.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.045015 restraints weight = 41275.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3536

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= 0.243
  Angle     :  0.777  11.970  17379  Z= 0.400
  Chirality :  0.046   0.227   1943
  Planarity :  0.006   0.066   1998
  Dihedral  : 17.587  84.566   2469
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 20.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.47 %
    Favored  : 84.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.22), residues: 1312
  helix: -0.23 (0.23), residues: 513
  sheet: -1.18 (0.69), residues: 51
  loop : -3.69 (0.20), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 725 
 HIS   0.009   0.002   HIS A 983 
 PHE   0.027   0.002   PHE A 970 
 TYR   0.060   0.002   TYR A 872 
 ARG   0.011   0.001   ARG A 548 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05036 (  449)
  hydrogen bonds       : angle       5.56211 ( 1220)
  covalent geometry    : bond        0.00507 (12655)
  covalent geometry    : angle       0.77692 (17379)

*********************** 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
  107 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  722 MET cc_start: 0.8756 (tmm) cc_final: 0.8470 (tmm)
REVERT: A  740 MET cc_start: 0.8254 (tpp) cc_final: 0.8018 (tpp)
REVERT: A  751 SER cc_start: 0.9562 (m) cc_final: 0.9348 (m)
REVERT: A  848 TRP cc_start: 0.8148 (m-90) cc_final: 0.7741 (m-90)
REVERT: A  920 CYS cc_start: 0.8755 (t) cc_final: 0.8482 (m)
REVERT: A  937 MET cc_start: 0.4205 (mpp) cc_final: 0.3835 (mpp)
REVERT: A 1011 MET cc_start: 0.9102 (mmm) cc_final: 0.8853 (tpp)
REVERT: A 1022 MET cc_start: 0.8693 (ptp) cc_final: 0.8485 (ptp)
REVERT: A 1040 MET cc_start: 0.9037 (mmt) cc_final: 0.8240 (mmt)
REVERT: A 1146 MET cc_start: 0.8862 (mpp) cc_final: 0.8381 (mpp)
REVERT: A 1241 MET cc_start: 0.9421 (mmm) cc_final: 0.9053 (mmt)
REVERT: A 1308 ARG cc_start: 0.8172 (ptt180) cc_final: 0.7809 (ptm160)
REVERT: A 1322 MET cc_start: 0.9050 (ttt) cc_final: 0.8809 (ttt)
REVERT: A 1330 GLU cc_start: 0.9038 (pt0) cc_final: 0.8769 (pt0)
REVERT: C  501 LYS cc_start: 0.7440 (pptt) cc_final: 0.6835 (mmmt)
REVERT: C  514 CYS cc_start: 0.9519 (m) cc_final: 0.9315 (m)
REVERT: C  520 MET cc_start: 0.8429 (mtp) cc_final: 0.7949 (mmm)
REVERT: C  530 TYR cc_start: 0.7820 (m-80) cc_final: 0.7307 (m-80)
REVERT: C  697 MET cc_start: 0.8014 (ptt) cc_final: 0.7675 (ptt)
REVERT: B  520 MET cc_start: 0.9032 (ttp) cc_final: 0.8307 (ttp)
REVERT: B  697 MET cc_start: 0.8626 (mmm) cc_final: 0.8203 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.2211
  time to fit residues: 36.2963
Evaluate side-chains
  86 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 89 optimal weight:    8.9990
   chunk 116 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 109 optimal weight:    9.9990
   chunk 85 optimal weight:   10.0000
   chunk 73 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   chunk 42 optimal weight:    0.5980
   chunk 104 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    4.9188

-------------------------------------------------------------------------------
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 774 HIS ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.055214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.042376 restraints weight = 97446.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.043788 restraints weight = 58260.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.044748 restraints weight = 41232.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3684

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= 0.238
  Angle     :  0.789  12.120  17379  Z= 0.404
  Chirality :  0.046   0.206   1943
  Planarity :  0.006   0.067   1998
  Dihedral  : 17.596  83.771   2469
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 20.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.70 %
    Favored  : 84.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.22), residues: 1312
  helix: -0.22 (0.23), residues: 512
  sheet: -1.59 (0.70), residues: 52
  loop : -3.62 (0.21), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 725 
 HIS   0.009   0.002   HIS A 983 
 PHE   0.032   0.002   PHE A 970 
 TYR   0.065   0.002   TYR A 872 
 ARG   0.013   0.001   ARG A 548 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05095 (  449)
  hydrogen bonds       : angle       5.55558 ( 1220)
  covalent geometry    : bond        0.00495 (12655)
  covalent geometry    : angle       0.78862 (17379)

*********************** 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
  103 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.293 
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  751 SER cc_start: 0.9563 (m) cc_final: 0.9340 (m)
REVERT: A  848 TRP cc_start: 0.8101 (m-90) cc_final: 0.7716 (m-90)
REVERT: A  920 CYS cc_start: 0.8742 (t) cc_final: 0.8441 (m)
REVERT: A  937 MET cc_start: 0.4100 (mpp) cc_final: 0.3143 (mtt)
REVERT: A 1011 MET cc_start: 0.9100 (mmm) cc_final: 0.8852 (tpp)
REVERT: A 1040 MET cc_start: 0.9050 (mmt) cc_final: 0.8306 (mmt)
REVERT: A 1235 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9273 (mm-30)
REVERT: A 1241 MET cc_start: 0.9458 (mmm) cc_final: 0.9046 (mmt)
REVERT: A 1308 ARG cc_start: 0.8007 (ptt180) cc_final: 0.7688 (ptt180)
REVERT: A 1322 MET cc_start: 0.9049 (ttt) cc_final: 0.8828 (ttt)
REVERT: A 1330 GLU cc_start: 0.8999 (pt0) cc_final: 0.8611 (pt0)
REVERT: C  501 LYS cc_start: 0.7385 (pptt) cc_final: 0.6845 (mmtm)
REVERT: C  520 MET cc_start: 0.8497 (mtp) cc_final: 0.8165 (ttp)
REVERT: C  697 MET cc_start: 0.7942 (ptt) cc_final: 0.7548 (ptt)
REVERT: B  520 MET cc_start: 0.9205 (ttp) cc_final: 0.8563 (ttp)
REVERT: B  697 MET cc_start: 0.8643 (mmm) cc_final: 0.8208 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.2191
  time to fit residues: 35.6498
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  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 112 optimal weight:    8.9990
   chunk 80 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0570
   chunk 2 optimal weight:   20.0000
   chunk 88 optimal weight:    0.0970
   chunk 18 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.4100

-------------------------------------------------------------------------------
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
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1042 ASN
A1080 ASN
** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 736 GLN
B 685 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.057937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.045255 restraints weight = 93706.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.046656 restraints weight = 58024.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.047622 restraints weight = 41528.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  12655  Z= 0.131
  Angle     :  0.719  12.351  17379  Z= 0.359
  Chirality :  0.043   0.213   1943
  Planarity :  0.005   0.068   1998
  Dihedral  : 17.219  80.170   2469
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.96 %
    Favored  : 87.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.23), residues: 1312
  helix:  0.04 (0.23), residues: 518
  sheet: -1.22 (0.68), residues: 56
  loop : -3.54 (0.21), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 665 
 HIS   0.010   0.001   HIS A 859 
 PHE   0.023   0.002   PHE A 970 
 TYR   0.050   0.002   TYR A 872 
 ARG   0.009   0.001   ARG B 670 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04340 (  449)
  hydrogen bonds       : angle       5.26728 ( 1220)
  covalent geometry    : bond        0.00289 (12655)
  covalent geometry    : angle       0.71935 (17379)

*********************** 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
  120 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.261 
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  618 CYS cc_start: 0.8462 (t) cc_final: 0.8245 (t)
REVERT: A  699 MET cc_start: 0.8935 (mmp) cc_final: 0.8564 (mmp)
REVERT: A  848 TRP cc_start: 0.7876 (m-90) cc_final: 0.7221 (m-90)
REVERT: A  937 MET cc_start: 0.4037 (mpp) cc_final: 0.3230 (mtt)
REVERT: A 1011 MET cc_start: 0.9038 (mmm) cc_final: 0.8800 (tpp)
REVERT: A 1022 MET cc_start: 0.8518 (ptp) cc_final: 0.8300 (ptp)
REVERT: A 1146 MET cc_start: 0.8878 (mpp) cc_final: 0.8487 (mpp)
REVERT: A 1235 GLU cc_start: 0.9424 (mt-10) cc_final: 0.9210 (mm-30)
REVERT: A 1241 MET cc_start: 0.9469 (mmm) cc_final: 0.9060 (mmt)
REVERT: A 1308 ARG cc_start: 0.8060 (ptt180) cc_final: 0.7658 (ptm160)
REVERT: C  514 CYS cc_start: 0.9436 (m) cc_final: 0.9231 (m)
REVERT: C  520 MET cc_start: 0.8483 (mtp) cc_final: 0.8156 (ttm)
REVERT: C  621 TYR cc_start: 0.9515 (t80) cc_final: 0.9282 (t80)
REVERT: C  666 CYS cc_start: 0.5289 (m) cc_final: 0.5041 (m)
REVERT: C  697 MET cc_start: 0.7819 (ptt) cc_final: 0.7527 (ptt)
REVERT: B  520 MET cc_start: 0.9195 (ttp) cc_final: 0.8554 (ppp)
REVERT: B  521 GLN cc_start: 0.9497 (mm110) cc_final: 0.8768 (tm-30)
REVERT: B  697 MET cc_start: 0.8556 (mmm) cc_final: 0.8070 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.2025
  time to fit residues: 37.8274
Evaluate side-chains
  95 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 130 optimal weight:    0.4980
   chunk 127 optimal weight:    4.9990
   chunk 112 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 51 optimal weight:    0.3980
   chunk 129 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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**
A1105 GLN
** 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 685 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.059361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.046765 restraints weight = 93088.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.048193 restraints weight = 58026.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.049143 restraints weight = 41567.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.4187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12655  Z= 0.122
  Angle     :  0.708  12.417  17379  Z= 0.350
  Chirality :  0.042   0.197   1943
  Planarity :  0.005   0.070   1998
  Dihedral  : 16.799  74.401   2469
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.65 %
    Favored  : 87.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.23), residues: 1312
  helix:  0.15 (0.23), residues: 526
  sheet: -0.93 (0.77), residues: 47
  loop : -3.53 (0.20), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 665 
 HIS   0.007   0.001   HIS A 774 
 PHE   0.024   0.001   PHE C 503 
 TYR   0.038   0.001   TYR A 872 
 ARG   0.007   0.000   ARG A 923 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04077 (  449)
  hydrogen bonds       : angle       5.01485 ( 1220)
  covalent geometry    : bond        0.00268 (12655)
  covalent geometry    : angle       0.70837 (17379)

********************** 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
  118 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.305 
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  618 CYS cc_start: 0.8412 (t) cc_final: 0.8004 (t)
REVERT: A  636 MET cc_start: 0.8351 (mmt) cc_final: 0.7784 (tpp)
REVERT: A  848 TRP cc_start: 0.7936 (m-90) cc_final: 0.7246 (m-90)
REVERT: A  862 MET cc_start: 0.9054 (mmm) cc_final: 0.8625 (mmm)
REVERT: A  937 MET cc_start: 0.3752 (mpp) cc_final: 0.2999 (mtt)
REVERT: A 1011 MET cc_start: 0.9036 (mmm) cc_final: 0.8781 (tpp)
REVERT: A 1146 MET cc_start: 0.8815 (mpp) cc_final: 0.8416 (mpp)
REVERT: A 1235 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9241 (mm-30)
REVERT: A 1241 MET cc_start: 0.9604 (mmm) cc_final: 0.9157 (mmt)
REVERT: A 1322 MET cc_start: 0.8904 (ttt) cc_final: 0.8627 (ttt)
REVERT: A 1330 GLU cc_start: 0.8331 (pt0) cc_final: 0.8109 (mm-30)
REVERT: C  520 MET cc_start: 0.8368 (mtp) cc_final: 0.7909 (mmm)
REVERT: C  666 CYS cc_start: 0.4944 (m) cc_final: 0.4408 (m)
REVERT: C  697 MET cc_start: 0.8187 (ptt) cc_final: 0.7915 (ptt)
REVERT: B  520 MET cc_start: 0.9122 (ttp) cc_final: 0.8509 (ppp)
REVERT: B  521 GLN cc_start: 0.9546 (mm110) cc_final: 0.8816 (tm-30)
REVERT: B  627 CYS cc_start: 0.9451 (m) cc_final: 0.9008 (p)
REVERT: B  682 GLN cc_start: 0.8963 (mm110) cc_final: 0.8650 (mt0)
REVERT: B  697 MET cc_start: 0.8564 (mmm) cc_final: 0.8096 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2062
  time to fit residues: 37.8397
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  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0770
   chunk 5 optimal weight:    9.9990
   chunk 91 optimal weight:    9.9990
   chunk 105 optimal weight:    8.9990
   chunk 123 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    2.1142

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

Flipped N/Q/H residues before XYZ refinement:
A 573 HIS
** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 924 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.058472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.045825 restraints weight = 94528.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.047210 restraints weight = 59120.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.048148 restraints weight = 42526.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.4222

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= 0.142
  Angle     :  0.701  12.564  17379  Z= 0.351
  Chirality :  0.043   0.344   1943
  Planarity :  0.005   0.068   1998
  Dihedral  : 16.740  73.765   2469
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.58 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.23), residues: 1312
  helix:  0.19 (0.23), residues: 527
  sheet: -0.76 (0.78), residues: 47
  loop : -3.49 (0.20), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 665 
 HIS   0.007   0.001   HIS A 774 
 PHE   0.083   0.002   PHE A 847 
 TYR   0.047   0.001   TYR A 872 
 ARG   0.006   0.000   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04135 (  449)
  hydrogen bonds       : angle       5.03566 ( 1220)
  covalent geometry    : bond        0.00308 (12655)
  covalent geometry    : angle       0.70071 (17379)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3869.21 seconds
wall clock time: 71 minutes 20.42 seconds (4280.42 seconds total)