Starting phenix.real_space_refine
on Wed Mar 12 10:54:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rqs_24635/03_2025/7rqs_24635.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rqs_24635/03_2025/7rqs_24635.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rqs_24635/03_2025/7rqs_24635.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rqs_24635/03_2025/7rqs_24635.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rqs_24635/03_2025/7rqs_24635.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rqs_24635/03_2025/7rqs_24635.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.028
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
     Mg      1      5.21       5
     S      48      5.16       5
     C    4898      2.51       5
     N    1349      2.21       5
     O    1496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7792
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1074, 7791
          Classifications: {'peptide': 1074}
          Incomplete info: {'truncation_to_alanine': 192}
          Link IDs: {'PTRANS': 38, 'TRANS': 1035}
          Chain breaks: 8
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 860
          Unresolved non-hydrogen angles: 1087
          Unresolved non-hydrogen dihedrals: 768
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 20, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 15, 'GLU:plan': 21, 'ARG:plan': 19}
          Unresolved non-hydrogen planarities: 522
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.34, per 1000 atoms: 0.94
  Number of scatterers: 7792
  At special positions: 0
  Unit cell: (81.024, 101.28, 108.454, 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      48     16.00
     Mg      1     11.99
     O    1496      8.00
     N    1349      7.00
     C    4898      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: 2.09
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2040

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 9 sheets defined
      38.2% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 34
      removed outlier: 3.546A  pdb=" N   LEU A  32 " --> pdb=" O   ARG A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 77
      removed outlier: 3.657A  pdb=" N   SER A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG A  69 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 103
      No H-bonds generated for 'chain 'A' and resid 101 through 103'
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 3.596A  pdb=" N   THR A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 273
    Processing helix  chain 'A' and resid 295 through 305
      removed outlier: 4.155A  pdb=" N   ALA A 301 " --> pdb=" O   PHE A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 315
    Processing helix  chain 'A' and resid 315 through 325
      removed outlier: 3.704A  pdb=" N   MET A 325 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 339
    Processing helix  chain 'A' and resid 346 through 356
    Processing helix  chain 'A' and resid 372 through 377
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 409 through 413
      removed outlier: 5.610A  pdb=" N   SER A 413 " --> pdb=" O   GLU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 434
      removed outlier: 3.531A  pdb=" N   LEU A 433 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 460
    Processing helix  chain 'A' and resid 475 through 481
    Processing helix  chain 'A' and resid 496 through 503
      removed outlier: 3.523A  pdb=" N   GLY A 503 " --> pdb=" O   ARG A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 521
      removed outlier: 4.438A  pdb=" N   LEU A 521 " --> pdb=" O   ARG A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 573
    Processing helix  chain 'A' and resid 632 through 643
    Processing helix  chain 'A' and resid 645 through 662
      removed outlier: 3.981A  pdb=" N   PHE A 649 " --> pdb=" O   GLU A 645 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLU A 650 " --> pdb=" O   ASP A 646 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ALA A 651 " --> pdb=" O   ALA A 647 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   MET A 652 " --> pdb=" O   MET A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 671
      removed outlier: 3.872A  pdb=" N   ALA A 669 " --> pdb=" O   ASP A 666 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU A 671 " --> pdb=" O   ASP A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 692
    Processing helix  chain 'A' and resid 699 through 720
    Processing helix  chain 'A' and resid 753 through 759
    Processing helix  chain 'A' and resid 802 through 807
    Processing helix  chain 'A' and resid 821 through 826
      removed outlier: 3.517A  pdb=" N   CYS A 826 " --> pdb=" O   HIS A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 882
    Processing helix  chain 'A' and resid 884 through 896
      removed outlier: 3.611A  pdb=" N   ILE A 888 " --> pdb=" O   THR A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 905 through 921
    Processing helix  chain 'A' and resid 931 through 935
    Processing helix  chain 'A' and resid 958 through 969
      removed outlier: 3.864A  pdb=" N   ARG A 962 " --> pdb=" O   GLY A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 991
      removed outlier: 3.812A  pdb=" N   GLU A 988 " --> pdb=" O   ASP A 984 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLU A 989 " --> pdb=" O   VAL A 985 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1018
      removed outlier: 4.259A  pdb=" N   ALA A1001 " --> pdb=" O   GLU A 997 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   GLU A1008 " --> pdb=" O   ASP A1004 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TYR A1017 " --> pdb=" O   LEU A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1068
      removed outlier: 3.563A  pdb=" N   ASP A1049 " --> pdb=" O   GLY A1045 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1089
    Processing helix  chain 'A' and resid 1101 through 1106
      removed outlier: 4.030A  pdb=" N   VAL A1106 " --> pdb=" O   PHE A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1117
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13
      removed outlier: 6.604A  pdb=" N   GLN A  60 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 221
      removed outlier: 4.018A  pdb=" N   MET A 218 " --> pdb=" O   VAL A 195 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL A 195 " --> pdb=" O   MET A 218 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE A 220 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS A 155 " --> pdb=" O   PHE A 192 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG A 142 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLU A 127 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL A 113 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   ILE A 109 " --> pdb=" O   GLY A 131 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ARG A 133 " --> pdb=" O   ASP A 107 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ASP A 107 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   TRP A 135 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ARG A 105 " --> pdb=" O   TRP A 135 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL A 110 " --> pdb=" O   GLU A 240 " (cutoff:3.500A)
      removed outlier: 9.155A  pdb=" N   LEU A 262 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   SER A 168 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 125
      removed outlier: 3.653A  pdb=" N   ALA A 125 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 400
      removed outlier: 5.527A  pdb=" N   LEU A 393 " --> pdb=" O   TYR A 385 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   TYR A 385 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   GLY A 395 " --> pdb=" O   ARG A 383 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ARG A 383 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   PHE A 415 " --> pdb=" O   SER A 380 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   GLN A 382 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ARG A 417 " --> pdb=" O   GLN A 382 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   TRP A 485 " --> pdb=" O   LEU A 472 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 526 through 530
      removed outlier: 4.655A  pdb=" N   LEU A 618 " --> pdb=" O   THR A 528 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 557 through 560
      removed outlier: 6.371A  pdb=" N   GLY A 558 " --> pdb=" O   ALA A 593 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ARG A 622 " --> pdb=" O   GLN A 582 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 628
      removed outlier: 4.384A  pdb=" N   MET A 627 " --> pdb=" O   ILE A 730 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE A 730 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   ILE A 812 " --> pdb=" O   ILE A 730 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ILE A 732 " --> pdb=" O   ILE A 812 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   PHE A 814 " --> pdb=" O   ILE A 732 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   CYS A 734 " --> pdb=" O   PHE A 814 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   CYS A 811 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ARG A 749 " --> pdb=" O   CYS A 811 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   VAL A 748 " --> pdb=" O   VAL A 775 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 628
      removed outlier: 4.384A  pdb=" N   MET A 627 " --> pdb=" O   ILE A 730 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE A 730 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   VAL A 748 " --> pdb=" O   VAL A 775 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 940
      removed outlier: 6.396A  pdb=" N   PHE A 939 " --> pdb=" O   TYR A 951 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    323 hydrogen bonds defined for protein.
    924 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.81

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2101
        1.33 -     1.45: 1219
        1.45 -     1.57: 4516
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 7910
  Sorted by residual:
  bond pdb=" C   ARG A  98 "
       pdb=" N   PRO A  99 "
    ideal  model  delta    sigma   weight residual
    1.332  1.367 -0.035 1.32e-02 5.74e+03 7.05e+00
  bond pdb=" N   VAL A 100 "
       pdb=" CA  VAL A 100 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.030 1.19e-02 7.06e+03 6.27e+00
  bond pdb=" N   ARG A  98 "
       pdb=" CA  ARG A  98 "
    ideal  model  delta    sigma   weight residual
    1.451  1.490 -0.039 1.70e-02 3.46e+03 5.23e+00
  bond pdb=" N   ARG A 103 "
       pdb=" CA  ARG A 103 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.33e-02 5.65e+03 4.77e+00
  bond pdb=" N   ASP A 101 "
       pdb=" CA  ASP A 101 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.76e-02 3.23e+03 3.00e+00
  ... (remaining 7905 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 10505
        1.56 -     3.11: 187
        3.11 -     4.67: 37
        4.67 -     6.23: 4
        6.23 -     7.78: 2
  Bond angle restraints: 10735
  Sorted by residual:
  angle pdb=" N   PRO A  99 "
        pdb=" CA  PRO A  99 "
        pdb=" CB  PRO A  99 "
      ideal   model   delta    sigma   weight residual
     103.34  106.68   -3.34 9.30e-01 1.16e+00 1.29e+01
  angle pdb=" CA  VAL A 100 "
        pdb=" C   VAL A 100 "
        pdb=" O   VAL A 100 "
      ideal   model   delta    sigma   weight residual
     120.95  117.68    3.27 1.04e+00 9.25e-01 9.86e+00
  angle pdb=" N   GLN A 570 "
        pdb=" CA  GLN A 570 "
        pdb=" CB  GLN A 570 "
      ideal   model   delta    sigma   weight residual
     110.16  114.68   -4.52 1.48e+00 4.57e-01 9.34e+00
  angle pdb=" N   PRO A  97 "
        pdb=" CA  PRO A  97 "
        pdb=" C   PRO A  97 "
      ideal   model   delta    sigma   weight residual
     112.47  118.50   -6.03 2.06e+00 2.36e-01 8.57e+00
  angle pdb=" CA  ILE A  96 "
        pdb=" C   ILE A  96 "
        pdb=" N   PRO A  97 "
      ideal   model   delta    sigma   weight residual
     119.42  122.14   -2.72 9.30e-01 1.16e+00 8.55e+00
  ... (remaining 10730 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 4328
       17.20 -    34.40: 377
       34.40 -    51.59: 80
       51.59 -    68.79: 9
       68.79 -    85.99: 3
  Dihedral angle restraints: 4797
    sinusoidal: 1675
      harmonic: 3122
  Sorted by residual:
  dihedral pdb=" CA  GLU A 117 "
           pdb=" C   GLU A 117 "
           pdb=" N   SER A 118 "
           pdb=" CA  SER A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.41   16.59     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  ASP A 174 "
           pdb=" CB  ASP A 174 "
           pdb=" CG  ASP A 174 "
           pdb=" OD1 ASP A 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.65   52.65     1      2.00e+01 2.50e-03 9.44e+00
  dihedral pdb=" N   VAL A 100 "
           pdb=" CA  VAL A 100 "
           pdb=" CB  VAL A 100 "
           pdb=" CG1 VAL A 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    8.22   51.78     3      1.50e+01 4.44e-03 9.05e+00
  ... (remaining 4794 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 928
       0.040 -    0.080: 247
       0.080 -    0.120: 89
       0.120 -    0.161: 6
       0.161 -    0.201: 3
  Chirality restraints: 1273
  Sorted by residual:
  chirality pdb=" CA  PRO A  97 "
            pdb=" N   PRO A  97 "
            pdb=" C   PRO A  97 "
            pdb=" CB  PRO A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  THR A 463 "
            pdb=" CA  THR A 463 "
            pdb=" OG1 THR A 463 "
            pdb=" CG2 THR A 463 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.64e-01
  chirality pdb=" CB  VAL A 100 "
            pdb=" CA  VAL A 100 "
            pdb=" CG1 VAL A 100 "
            pdb=" CG2 VAL A 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.60e-01
  ... (remaining 1270 not shown)

  Planarity restraints: 1400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 845 "    0.066 5.00e-02 4.00e+02   9.90e-02 1.57e+01
        pdb=" N   PRO A 846 "   -0.171 5.00e-02 4.00e+02
        pdb=" CA  PRO A 846 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 846 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 850 "   -0.035 5.00e-02 4.00e+02   5.38e-02 4.64e+00
        pdb=" N   PRO A 851 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 851 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 851 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 346 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO A 347 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 347 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 347 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1397 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 90
        2.65 -     3.21: 7505
        3.21 -     3.78: 11846
        3.78 -     4.34: 15587
        4.34 -     4.90: 25512
  Nonbonded interactions: 60540
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 832 "
            pdb="MG    MG A1201 "
     model   vdw
     2.088 2.170
  nonbonded pdb=" O   SER A 682 "
            pdb=" NZ  LYS A 688 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" O   ALA A 432 "
            pdb=" OG1 THR A 448 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" NH2 ARG A 506 "
            pdb=" O   ASP A 612 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   GLY A 503 "
            pdb=" NH1 ARG A 506 "
     model   vdw
     2.267 3.120
  ... (remaining 60535 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             7.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.810
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
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      :  0.002   0.039   7910  Z= 0.172
  Angle     :  0.544   7.784  10735  Z= 0.301
  Chirality :  0.041   0.201   1273
  Planarity :  0.004   0.099   1400
  Dihedral  : 13.383  85.988   2757
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.00 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.26), residues: 1057
  helix:  1.27 (0.29), residues: 354
  sheet: -1.41 (0.44), residues: 142
  loop : -1.67 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 129 
 HIS   0.002   0.001   HIS A 710 
 PHE   0.010   0.001   PHE A 471 
 TYR   0.023   0.001   TYR A 799 
 ARG   0.007   0.000   ARG A 766 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 154
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 CYS cc_start: 0.6585 (t) cc_final: 0.6292 (t)
REVERT: A  281 LEU cc_start: 0.7121 (mp) cc_final: 0.6820 (mp)
REVERT: A  282 LEU cc_start: 0.7430 (mt) cc_final: 0.7166 (mt)
REVERT: A  328 GLU cc_start: 0.6633 (mp0) cc_final: 0.6331 (mp0)
REVERT: A  355 MET cc_start: 0.4699 (tpt) cc_final: 0.4496 (tpt)
REVERT: A  424 ASP cc_start: 0.7269 (p0) cc_final: 0.7033 (p0)
REVERT: A  487 PHE cc_start: 0.7627 (t80) cc_final: 0.7414 (t80)
REVERT: A  879 TYR cc_start: 0.7266 (t80) cc_final: 0.6828 (t80)
REVERT: A  883 ASP cc_start: 0.7864 (t70) cc_final: 0.7378 (t0)
REVERT: A  897 ASP cc_start: 0.7638 (m-30) cc_final: 0.7179 (m-30)
REVERT: A  907 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7538 (mtmt)
  outliers start: 2
  outliers final: 1
  residues processed: 156
  average time/residue: 0.1929
  time to fit residues: 41.1525
Evaluate side-chains
  137 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.175239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.148714 restraints weight = 10726.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.152752 restraints weight = 5994.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.155392 restraints weight = 4021.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7910  Z= 0.296
  Angle     :  0.597   8.466  10735  Z= 0.317
  Chirality :  0.044   0.182   1273
  Planarity :  0.005   0.062   1400
  Dihedral  :  4.561  33.220   1125
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.76 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.25), residues: 1057
  helix:  0.55 (0.27), residues: 365
  sheet: -1.40 (0.45), residues: 139
  loop : -1.73 (0.25), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 485 
 HIS   0.007   0.001   HIS A 411 
 PHE   0.021   0.002   PHE A 471 
 TYR   0.014   0.002   TYR A 747 
 ARG   0.004   0.001   ARG A 453 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7543 (mtmt)
REVERT: A  153 CYS cc_start: 0.6634 (t) cc_final: 0.6318 (t)
REVERT: A  239 LEU cc_start: 0.8096 (mt) cc_final: 0.7863 (mt)
REVERT: A  282 LEU cc_start: 0.7550 (mt) cc_final: 0.7249 (mt)
REVERT: A  346 ASP cc_start: 0.6608 (p0) cc_final: 0.6342 (p0)
REVERT: A  355 MET cc_start: 0.4967 (tpt) cc_final: 0.4643 (tpt)
REVERT: A  424 ASP cc_start: 0.7332 (p0) cc_final: 0.7043 (p0)
REVERT: A  662 ASN cc_start: 0.7510 (m-40) cc_final: 0.7287 (m-40)
REVERT: A  688 LYS cc_start: 0.7488 (mptt) cc_final: 0.6798 (mptt)
REVERT: A  870 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6625 (tm-30)
REVERT: A  880 MET cc_start: 0.7303 (tpp) cc_final: 0.6611 (mpp)
REVERT: A  883 ASP cc_start: 0.8006 (t70) cc_final: 0.7572 (t0)
REVERT: A  907 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7696 (mtmt)
REVERT: A  923 LYS cc_start: 0.7734 (mtmm) cc_final: 0.7409 (mtmm)
REVERT: A  957 PHE cc_start: 0.5207 (p90) cc_final: 0.3292 (p90)
  outliers start: 13
  outliers final: 7
  residues processed: 156
  average time/residue: 0.1789
  time to fit residues: 39.1419
Evaluate side-chains
  155 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 148
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  924 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0670
   chunk 103 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
** A  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.173079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.146772 restraints weight = 10895.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.150688 restraints weight = 6069.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.153342 restraints weight = 4067.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   7910  Z= 0.386
  Angle     :  0.632   8.620  10735  Z= 0.338
  Chirality :  0.046   0.174   1273
  Planarity :  0.005   0.051   1400
  Dihedral  :  4.914  23.840   1125
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.91 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.25), residues: 1057
  helix:  0.24 (0.27), residues: 373
  sheet: -1.43 (0.44), residues: 136
  loop : -1.86 (0.25), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 485 
 HIS   0.006   0.001   HIS A 411 
 PHE   0.024   0.002   PHE A 471 
 TYR   0.024   0.002   TYR A 879 
 ARG   0.003   0.000   ARG A 898 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 LEU cc_start: 0.7567 (mt) cc_final: 0.7313 (mt)
REVERT: A  328 GLU cc_start: 0.6755 (mp0) cc_final: 0.6384 (mp0)
REVERT: A  346 ASP cc_start: 0.6624 (p0) cc_final: 0.6308 (p0)
REVERT: A  355 MET cc_start: 0.4999 (tpt) cc_final: 0.4612 (tpt)
REVERT: A  424 ASP cc_start: 0.7274 (p0) cc_final: 0.7004 (p0)
REVERT: A  496 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6788 (mm-30)
REVERT: A  554 SER cc_start: 0.7037 (p) cc_final: 0.6712 (p)
REVERT: A  663 MET cc_start: 0.8406 (ptm) cc_final: 0.8144 (ttp)
REVERT: A  878 ASP cc_start: 0.7320 (m-30) cc_final: 0.6982 (m-30)
REVERT: A  883 ASP cc_start: 0.8052 (t70) cc_final: 0.7602 (t0)
REVERT: A  907 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7727 (mtmt)
REVERT: A  923 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7430 (mtmm)
REVERT: A  957 PHE cc_start: 0.5619 (p90) cc_final: 0.3745 (p90)
  outliers start: 15
  outliers final: 9
  residues processed: 161
  average time/residue: 0.1931
  time to fit residues: 43.0865
Evaluate side-chains
  157 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 147
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  496 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  924 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 39 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.174958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.148819 restraints weight = 10798.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.152838 restraints weight = 6145.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.155388 restraints weight = 4120.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6689
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7910  Z= 0.221
  Angle     :  0.551  11.850  10735  Z= 0.290
  Chirality :  0.042   0.183   1273
  Planarity :  0.004   0.059   1400
  Dihedral  :  4.457  19.510   1124
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.14 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.34 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.26), residues: 1057
  helix:  0.59 (0.28), residues: 367
  sheet: -1.46 (0.43), residues: 145
  loop : -1.76 (0.25), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 623 
 HIS   0.009   0.001   HIS A 411 
 PHE   0.020   0.002   PHE A 471 
 TYR   0.021   0.001   TYR A 879 
 ARG   0.002   0.000   ARG A 766 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.5377 (tt0) cc_final: 0.5155 (tt0)
REVERT: A  282 LEU cc_start: 0.7561 (mt) cc_final: 0.7331 (mt)
REVERT: A  328 GLU cc_start: 0.6738 (mp0) cc_final: 0.6341 (mp0)
REVERT: A  346 ASP cc_start: 0.6521 (p0) cc_final: 0.6217 (p0)
REVERT: A  355 MET cc_start: 0.4910 (tpt) cc_final: 0.4536 (tpt)
REVERT: A  424 ASP cc_start: 0.7234 (p0) cc_final: 0.6921 (p0)
REVERT: A  496 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6677 (mm-30)
REVERT: A  554 SER cc_start: 0.7034 (p) cc_final: 0.6828 (p)
REVERT: A  724 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8098 (tp)
REVERT: A  730 ILE cc_start: 0.8197 (mt) cc_final: 0.7756 (mm)
REVERT: A  869 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6394 (mt)
REVERT: A  880 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6347 (mpp)
REVERT: A  883 ASP cc_start: 0.8014 (t70) cc_final: 0.7519 (t0)
REVERT: A  923 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7372 (mtmm)
REVERT: A  935 LYS cc_start: 0.8234 (mmmm) cc_final: 0.7954 (mmmm)
REVERT: A  957 PHE cc_start: 0.5648 (p90) cc_final: 0.3712 (p90)
  outliers start: 13
  outliers final: 4
  residues processed: 150
  average time/residue: 0.2193
  time to fit residues: 45.2861
Evaluate side-chains
  157 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  496 GLU
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  880 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 1 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 81 optimal weight:    0.4980
   chunk 100 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.173586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.147069 restraints weight = 10825.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.151013 restraints weight = 6035.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.153660 restraints weight = 4053.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7910  Z= 0.293
  Angle     :  0.587  10.703  10735  Z= 0.310
  Chirality :  0.044   0.165   1273
  Planarity :  0.005   0.051   1400
  Dihedral  :  4.638  19.873   1124
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.80 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.34 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.25), residues: 1057
  helix:  0.43 (0.27), residues: 372
  sheet: -1.50 (0.42), residues: 145
  loop : -1.82 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 485 
 HIS   0.009   0.001   HIS A 411 
 PHE   0.023   0.002   PHE A 471 
 TYR   0.024   0.002   TYR A 879 
 ARG   0.004   0.000   ARG A 605 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7856 (m)
REVERT: A  282 LEU cc_start: 0.7569 (mt) cc_final: 0.7337 (mt)
REVERT: A  328 GLU cc_start: 0.6778 (mp0) cc_final: 0.6374 (mp0)
REVERT: A  355 MET cc_start: 0.4914 (tpt) cc_final: 0.4599 (tpt)
REVERT: A  424 ASP cc_start: 0.7255 (p0) cc_final: 0.6938 (p0)
REVERT: A  478 GLN cc_start: 0.7634 (tt0) cc_final: 0.7207 (tt0)
REVERT: A  496 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6732 (mm-30)
REVERT: A  554 SER cc_start: 0.7146 (p) cc_final: 0.6855 (p)
REVERT: A  724 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8067 (tp)
REVERT: A  869 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6409 (mt)
REVERT: A  880 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6378 (mpp)
REVERT: A  883 ASP cc_start: 0.8072 (t70) cc_final: 0.7580 (t0)
REVERT: A  923 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7412 (mtmm)
REVERT: A  935 LYS cc_start: 0.8227 (mmmm) cc_final: 0.8016 (mmmm)
REVERT: A  957 PHE cc_start: 0.5652 (p90) cc_final: 0.3801 (p90)
  outliers start: 27
  outliers final: 17
  residues processed: 160
  average time/residue: 0.1740
  time to fit residues: 39.0594
Evaluate side-chains
  172 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  316 MET
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  483 SER
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  496 GLU
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  880 MET
Chi-restraints excluded: chain A residue  924 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0980
   chunk 60 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 713 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.175905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.149550 restraints weight = 10888.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.153597 restraints weight = 6017.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.155973 restraints weight = 4021.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7910  Z= 0.177
  Angle     :  0.540  10.912  10735  Z= 0.279
  Chirality :  0.042   0.160   1273
  Planarity :  0.004   0.050   1400
  Dihedral  :  4.266  18.589   1124
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.66 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.18 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.26), residues: 1057
  helix:  0.75 (0.28), residues: 368
  sheet: -1.41 (0.43), residues: 145
  loop : -1.75 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 623 
 HIS   0.008   0.001   HIS A 411 
 PHE   0.022   0.001   PHE A 957 
 TYR   0.021   0.001   TYR A 879 
 ARG   0.002   0.000   ARG A 605 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7750 (m)
REVERT: A  282 LEU cc_start: 0.7557 (mt) cc_final: 0.7349 (mt)
REVERT: A  328 GLU cc_start: 0.6768 (mp0) cc_final: 0.6334 (mp0)
REVERT: A  355 MET cc_start: 0.4918 (tpt) cc_final: 0.4629 (tpt)
REVERT: A  424 ASP cc_start: 0.7224 (p0) cc_final: 0.6954 (p0)
REVERT: A  496 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6718 (mm-30)
REVERT: A  554 SER cc_start: 0.7154 (p) cc_final: 0.6873 (p)
REVERT: A  724 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8011 (tp)
REVERT: A  762 GLN cc_start: 0.8365 (mp10) cc_final: 0.7868 (mp10)
REVERT: A  880 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6230 (mpp)
REVERT: A  883 ASP cc_start: 0.8057 (t70) cc_final: 0.7546 (t0)
REVERT: A  897 ASP cc_start: 0.7822 (m-30) cc_final: 0.7277 (m-30)
REVERT: A  923 LYS cc_start: 0.7682 (mtmm) cc_final: 0.7360 (mtmm)
REVERT: A  957 PHE cc_start: 0.5656 (p90) cc_final: 0.3603 (p90)
  outliers start: 20
  outliers final: 13
  residues processed: 168
  average time/residue: 0.2051
  time to fit residues: 48.7456
Evaluate side-chains
  168 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  316 MET
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  496 GLU
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  880 MET
Chi-restraints excluded: chain A residue  959 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 99 optimal weight:   20.0000
   chunk 92 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 824 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.174781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.148341 restraints weight = 10866.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.152308 restraints weight = 6063.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.154965 restraints weight = 4057.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6702
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7910  Z= 0.229
  Angle     :  0.562  10.527  10735  Z= 0.292
  Chirality :  0.042   0.165   1273
  Planarity :  0.004   0.050   1400
  Dihedral  :  4.347  19.272   1124
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.42 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.58 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.26), residues: 1057
  helix:  0.72 (0.28), residues: 372
  sheet: -1.35 (0.43), residues: 145
  loop : -1.78 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 623 
 HIS   0.009   0.001   HIS A 411 
 PHE   0.020   0.002   PHE A 471 
 TYR   0.023   0.002   TYR A 879 
 ARG   0.003   0.000   ARG A 605 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7770 (m)
REVERT: A  282 LEU cc_start: 0.7573 (mt) cc_final: 0.7362 (mt)
REVERT: A  355 MET cc_start: 0.4907 (tpt) cc_final: 0.4594 (tpt)
REVERT: A  424 ASP cc_start: 0.7259 (p0) cc_final: 0.6983 (p0)
REVERT: A  496 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6766 (mm-30)
REVERT: A  554 SER cc_start: 0.7171 (p) cc_final: 0.6845 (p)
REVERT: A  724 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8033 (tp)
REVERT: A  762 GLN cc_start: 0.8381 (mp10) cc_final: 0.7880 (mp10)
REVERT: A  869 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6252 (mt)
REVERT: A  880 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6285 (mpp)
REVERT: A  883 ASP cc_start: 0.8089 (t70) cc_final: 0.7600 (t0)
REVERT: A  897 ASP cc_start: 0.7831 (m-30) cc_final: 0.7291 (m-30)
REVERT: A  923 LYS cc_start: 0.7715 (mtmm) cc_final: 0.7399 (mtmm)
REVERT: A  957 PHE cc_start: 0.5633 (p90) cc_final: 0.3591 (p90)
  outliers start: 25
  outliers final: 14
  residues processed: 164
  average time/residue: 0.1817
  time to fit residues: 41.5990
Evaluate side-chains
  166 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  316 MET
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  496 GLU
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  880 MET
Chi-restraints excluded: chain A residue  924 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 102 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0670
   chunk 58 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0980
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 835 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.176890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.150684 restraints weight = 10862.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.154638 restraints weight = 6121.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.157267 restraints weight = 4120.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6656
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7910  Z= 0.164
  Angle     :  0.532   9.913  10735  Z= 0.274
  Chirality :  0.041   0.160   1273
  Planarity :  0.004   0.049   1400
  Dihedral  :  4.112  18.417   1124
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.28 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.03 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.26), residues: 1057
  helix:  0.90 (0.28), residues: 370
  sheet: -1.30 (0.43), residues: 147
  loop : -1.69 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 623 
 HIS   0.009   0.001   HIS A 411 
 PHE   0.023   0.001   PHE A 957 
 TYR   0.021   0.001   TYR A 879 
 ARG   0.002   0.000   ARG A 605 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7711 (m)
REVERT: A  355 MET cc_start: 0.4879 (tpt) cc_final: 0.4580 (tpt)
REVERT: A  399 GLU cc_start: 0.6906 (pt0) cc_final: 0.6690 (pt0)
REVERT: A  424 ASP cc_start: 0.7227 (p0) cc_final: 0.6951 (p0)
REVERT: A  554 SER cc_start: 0.7171 (p) cc_final: 0.6858 (p)
REVERT: A  559 LYS cc_start: 0.7086 (ptpp) cc_final: 0.6785 (ptpp)
REVERT: A  688 LYS cc_start: 0.7472 (mptt) cc_final: 0.6833 (mptt)
REVERT: A  762 GLN cc_start: 0.8345 (mp10) cc_final: 0.7882 (mp10)
REVERT: A  869 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6241 (mt)
REVERT: A  880 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6233 (mpp)
REVERT: A  883 ASP cc_start: 0.8054 (t70) cc_final: 0.7548 (t0)
REVERT: A  957 PHE cc_start: 0.5602 (p90) cc_final: 0.3553 (p90)
  outliers start: 17
  outliers final: 12
  residues processed: 160
  average time/residue: 0.1777
  time to fit residues: 39.2565
Evaluate side-chains
  165 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  316 MET
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  880 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 57 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0870
   chunk 31 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0670
   chunk 87 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 713 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.177322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.151070 restraints weight = 11116.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.155114 restraints weight = 6134.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.157745 restraints weight = 4074.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6649
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7910  Z= 0.158
  Angle     :  0.536   9.532  10735  Z= 0.274
  Chirality :  0.041   0.158   1273
  Planarity :  0.004   0.049   1400
  Dihedral  :  4.033  18.463   1124
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.10 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.64 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.26), residues: 1057
  helix:  0.98 (0.28), residues: 371
  sheet: -1.13 (0.44), residues: 142
  loop : -1.64 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 623 
 HIS   0.009   0.001   HIS A 411 
 PHE   0.022   0.001   PHE A 957 
 TYR   0.023   0.001   TYR A 345 
 ARG   0.002   0.000   ARG A 605 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7681 (m)
REVERT: A  355 MET cc_start: 0.4924 (tpt) cc_final: 0.4602 (tpt)
REVERT: A  399 GLU cc_start: 0.6906 (pt0) cc_final: 0.6687 (pt0)
REVERT: A  424 ASP cc_start: 0.7271 (p0) cc_final: 0.6997 (p0)
REVERT: A  554 SER cc_start: 0.7192 (p) cc_final: 0.6866 (p)
REVERT: A  762 GLN cc_start: 0.8320 (mp10) cc_final: 0.7882 (mp10)
REVERT: A  869 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6210 (mt)
REVERT: A  880 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6251 (mpp)
REVERT: A  883 ASP cc_start: 0.8055 (t70) cc_final: 0.7584 (t0)
REVERT: A  897 ASP cc_start: 0.7848 (m-30) cc_final: 0.7335 (m-30)
REVERT: A  907 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7563 (mtmt)
REVERT: A  957 PHE cc_start: 0.5565 (p90) cc_final: 0.3437 (p90)
  outliers start: 19
  outliers final: 13
  residues processed: 159
  average time/residue: 0.1976
  time to fit residues: 43.9889
Evaluate side-chains
  161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  316 MET
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  880 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 52 optimal weight:    0.0980
   chunk 95 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 713 GLN
A 835 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.175288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.148983 restraints weight = 10969.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.152962 restraints weight = 6136.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.155601 restraints weight = 4103.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7910  Z= 0.250
  Angle     :  0.594   9.498  10735  Z= 0.303
  Chirality :  0.043   0.184   1273
  Planarity :  0.004   0.050   1400
  Dihedral  :  4.267  18.781   1124
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.23 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.16 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.26), residues: 1057
  helix:  0.87 (0.28), residues: 370
  sheet: -1.19 (0.43), residues: 145
  loop : -1.72 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 485 
 HIS   0.010   0.001   HIS A 411 
 PHE   0.021   0.002   PHE A 471 
 TYR   0.032   0.002   TYR A 345 
 ARG   0.003   0.000   ARG A 605 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 1.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7766 (m)
REVERT: A  355 MET cc_start: 0.4908 (tpt) cc_final: 0.4587 (tpt)
REVERT: A  399 GLU cc_start: 0.6978 (pt0) cc_final: 0.6772 (pt0)
REVERT: A  424 ASP cc_start: 0.7271 (p0) cc_final: 0.6994 (p0)
REVERT: A  554 SER cc_start: 0.7217 (p) cc_final: 0.6882 (p)
REVERT: A  762 GLN cc_start: 0.8330 (mp10) cc_final: 0.7882 (mp10)
REVERT: A  869 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6273 (mt)
REVERT: A  870 GLU cc_start: 0.6767 (tm-30) cc_final: 0.6564 (tm-30)
REVERT: A  880 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6316 (mpp)
REVERT: A  883 ASP cc_start: 0.8099 (t70) cc_final: 0.7603 (t0)
REVERT: A  957 PHE cc_start: 0.5582 (p90) cc_final: 0.3591 (p90)
  outliers start: 17
  outliers final: 14
  residues processed: 157
  average time/residue: 0.2576
  time to fit residues: 56.7962
Evaluate side-chains
  161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  316 MET
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  880 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 1 optimal weight:   20.0000
   chunk 94 optimal weight:   20.0000
   chunk 88 optimal weight:    0.9980
   chunk 104 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 713 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.175225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.149078 restraints weight = 10922.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.152946 restraints weight = 6192.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.155557 restraints weight = 4181.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7910  Z= 0.243
  Angle     :  0.596   9.690  10735  Z= 0.306
  Chirality :  0.043   0.175   1273
  Planarity :  0.004   0.050   1400
  Dihedral  :  4.332  19.254   1124
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.51 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.11 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.26), residues: 1057
  helix:  0.78 (0.28), residues: 374
  sheet: -1.26 (0.43), residues: 145
  loop : -1.77 (0.26), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 485 
 HIS   0.009   0.001   HIS A 411 
 PHE   0.021   0.002   PHE A 471 
 TYR   0.030   0.002   TYR A 345 
 ARG   0.003   0.000   ARG A 605 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4788.24 seconds
wall clock time: 85 minutes 43.52 seconds (5143.52 seconds total)