Starting phenix.real_space_refine
on Wed Jan 15 00:57:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xxw_38763/01_2025/8xxw_38763.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xxw_38763/01_2025/8xxw_38763.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xxw_38763/01_2025/8xxw_38763.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xxw_38763/01_2025/8xxw_38763.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xxw_38763/01_2025/8xxw_38763.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xxw_38763/01_2025/8xxw_38763.cif"
  }
  resolution = 3.03
  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=   0.001 sd=   0.018
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
     Zn      1      6.06       5
     S      41      5.16       5
     C    4932      2.51       5
     N    1278      2.21       5
     O    1471      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 7723
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4595
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 561, 4588
          Classifications: {'peptide': 561}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 537}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 561, 4588
          Classifications: {'peptide': 561}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 537}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 4703
    Chain: "E"
      Number of atoms: 1300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1300
          Classifications: {'peptide': 162}
          Link IDs: {'PTRANS': 8, 'TRANS': 153}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 940
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 845
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' ZN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.38, per 1000 atoms: 0.96
  Number of scatterers: 7723
  At special positions: 0
  Unit cell: (70.55, 86.7, 141.1, 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)
     Zn      1     29.99
     S      41     16.00
     O    1471      8.00
     N    1278      7.00
     C    4932      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG A 902 " - " ASN A 546 "
      " NAG A 903 " - " ASN A  90 "
      " NAG E 701 " - " ASN E 343 "
  Time building additional restraints: 2.19
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "


  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1774

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 9 sheets defined
      50.0% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 52
      removed outlier: 3.590A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 4.021A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 88'
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.891A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.989A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 127
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 193
      removed outlier: 3.747A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 219 through 252
      removed outlier: 4.157A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.690A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.735A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.975A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 3.740A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.245A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 4.478A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 503
    Processing helix  chain 'A' and resid 505 through 509
      removed outlier: 3.723A  pdb=" N   ASP A 509 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.837A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.932A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.607A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'E' and resid 337 through 343
      removed outlier: 3.712A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 367 through 371
    Processing helix  chain 'E' and resid 406 through 410
    Processing helix  chain 'E' and resid 416 through 422
    Processing helix  chain 'E' and resid 438 through 443
      removed outlier: 3.586A  pdb=" N   SER E 443 " --> pdb=" O   ASN E 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 502 through 505
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.944A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 104
      removed outlier: 3.570A  pdb=" N   GLY H 103 " --> pdb=" O   ASP H 100 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.593A  pdb=" N   MET L  83 " --> pdb=" O   TYR L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.039A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.129A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358
    Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.579A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.482A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY L  84 " --> pdb=" O   LEU L 104 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1028 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: 2.33

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2473
        1.34 -     1.46: 1947
        1.46 -     1.58: 3437
        1.58 -     1.69: 1
        1.69 -     1.81: 67
  Bond restraints: 7925
  Sorted by residual:
  bond pdb=" C   LEU A 262 "
       pdb=" N   PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.331  1.360 -0.029 1.31e-02 5.83e+03 4.99e+00
  bond pdb=" N   ASP E 428 "
       pdb=" CA  ASP E 428 "
    ideal  model  delta    sigma   weight residual
    1.463  1.490 -0.027 1.31e-02 5.83e+03 4.27e+00
  bond pdb=" N   LEU A 262 "
       pdb=" CA  LEU A 262 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.024 1.41e-02 5.03e+03 2.93e+00
  bond pdb=" C1  NAG E 701 "
       pdb=" O5  NAG E 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.12e+00
  bond pdb=" C1  NAG A 902 "
       pdb=" O5  NAG A 902 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.81e+00
  ... (remaining 7920 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 10421
        1.36 -     2.72: 241
        2.72 -     4.07: 63
        4.07 -     5.43: 18
        5.43 -     6.79: 4
  Bond angle restraints: 10747
  Sorted by residual:
  angle pdb=" O   CYS A 261 "
        pdb=" C   CYS A 261 "
        pdb=" N   LEU A 262 "
      ideal   model   delta    sigma   weight residual
     123.10  127.10   -4.00 1.15e+00 7.56e-01 1.21e+01
  angle pdb=" N   GLY H 103 "
        pdb=" CA  GLY H 103 "
        pdb=" C   GLY H 103 "
      ideal   model   delta    sigma   weight residual
     115.46  110.53    4.93 1.63e+00 3.76e-01 9.14e+00
  angle pdb=" CA  MET A 270 "
        pdb=" CB  MET A 270 "
        pdb=" CG  MET A 270 "
      ideal   model   delta    sigma   weight residual
     114.10  120.00   -5.90 2.00e+00 2.50e-01 8.71e+00
  angle pdb=" CA  PRO A 500 "
        pdb=" N   PRO A 500 "
        pdb=" CD  PRO A 500 "
      ideal   model   delta    sigma   weight residual
     112.00  107.93    4.07 1.40e+00 5.10e-01 8.46e+00
  angle pdb=" CA  CYS A 261 "
        pdb=" C   CYS A 261 "
        pdb=" N   LEU A 262 "
      ideal   model   delta    sigma   weight residual
     115.55  111.87    3.68 1.33e+00 5.65e-01 7.67e+00
  ... (remaining 10742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 4085
       17.19 -    34.37: 453
       34.37 -    51.56: 137
       51.56 -    68.75: 26
       68.75 -    85.94: 9
  Dihedral angle restraints: 4710
    sinusoidal: 1935
      harmonic: 2775
  Sorted by residual:
  dihedral pdb=" CA  ASP A 597 "
           pdb=" CB  ASP A 597 "
           pdb=" CG  ASP A 597 "
           pdb=" OD1 ASP A 597 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.84   57.84     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CA  TYR H  60 "
           pdb=" C   TYR H  60 "
           pdb=" N   ASP H  61 "
           pdb=" CA  ASP H  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -59.17  -26.83     1      1.00e+01 1.00e-02 1.03e+01
  ... (remaining 4707 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 791
       0.038 -    0.076: 247
       0.076 -    0.114: 82
       0.114 -    0.152: 11
       0.152 -    0.190: 1
  Chirality restraints: 1132
  Sorted by residual:
  chirality pdb=" CA  LEU A 262 "
            pdb=" N   LEU A 262 "
            pdb=" C   LEU A 262 "
            pdb=" CB  LEU A 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.00e-01
  chirality pdb=" CA  ARG A 192 "
            pdb=" N   ARG A 192 "
            pdb=" C   ARG A 192 "
            pdb=" CB  ARG A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  PRO A 500 "
            pdb=" N   PRO A 500 "
            pdb=" C   PRO A 500 "
            pdb=" CB  PRO A 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.14 2.00e-01 2.50e+01 5.22e-01
  ... (remaining 1129 not shown)

  Planarity restraints: 1388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 499 "    0.057 5.00e-02 4.00e+02   8.45e-02 1.14e+01
        pdb=" N   PRO A 500 "   -0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H  61 "    0.049 5.00e-02 4.00e+02   7.39e-02 8.73e+00
        pdb=" N   PRO H  62 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO H  62 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO H  62 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H  52 "    0.039 5.00e-02 4.00e+02   6.03e-02 5.82e+00
        pdb=" N   PRO H  53 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO H  53 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO H  53 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1385 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 817
        2.75 -     3.29: 7301
        3.29 -     3.82: 12512
        3.82 -     4.36: 14663
        4.36 -     4.90: 25812
  Nonbonded interactions: 61105
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 269 "
            pdb=" N   GLY A 272 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OG  SER E 438 "
            pdb=" OD2 ASP E 442 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OH  TYR A 279 "
            pdb=" OD1 ASN A 290 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" N   GLU A 430 "
            pdb=" OE1 GLU A 430 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   SER H   7 "
            pdb=" OG1 THR H 116 "
     model   vdw
     2.303 3.040
  ... (remaining 61100 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.24 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.990
  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:          0.140
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     25.350
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7925  Z= 0.188
  Angle     :  0.567   6.790  10747  Z= 0.306
  Chirality :  0.041   0.190   1132
  Planarity :  0.005   0.084   1385
  Dihedral  : 16.104  85.937   2918
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 19.42 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.00 (0.28), residues: 935
  helix:  1.22 (0.27), residues: 390
  sheet:  0.91 (0.39), residues: 179
  loop :  0.07 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.029   0.001   PHE A 504 
 TYR   0.012   0.001   TYR A  50 
 ARG   0.003   0.000   ARG A 306 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 GLN cc_start: 0.8402 (mp10) cc_final: 0.8155 (mp10)
REVERT: E  443 SER cc_start: 0.8660 (m) cc_final: 0.8331 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2322
  time to fit residues: 46.9193
Evaluate side-chains
  153 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.0770
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0040
   chunk 48 optimal weight:    0.7980
   chunk 38 optimal weight:    0.2980
   chunk 73 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.3350

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  63 ASN
E 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.111715 restraints weight = 10885.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.07
r_work: 0.3294 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.0874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7925  Z= 0.181
  Angle     :  0.515   8.497  10747  Z= 0.270
  Chirality :  0.041   0.129   1132
  Planarity :  0.005   0.062   1385
  Dihedral  :  4.229  34.448   1099
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 18.58 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.16 (0.27), residues: 935
  helix:  1.25 (0.26), residues: 392
  sheet:  0.96 (0.39), residues: 181
  loop :  0.29 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.013   0.001   PHE H  99 
 TYR   0.017   0.001   TYR A 243 
 ARG   0.005   0.000   ARG A 219 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 165
  time to evaluate  : 0.859 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5205 (mmp) cc_final: 0.4548 (mmm)
REVERT: A  183 TYR cc_start: 0.7224 (t80) cc_final: 0.6869 (t80)
REVERT: E  443 SER cc_start: 0.8615 (m) cc_final: 0.8241 (p)
  outliers start: 8
  outliers final: 4
  residues processed: 168
  average time/residue: 0.2344
  time to fit residues: 51.1034
Evaluate side-chains
  174 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 170
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain L residue   10 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0470
   chunk 91 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0570
   chunk 40 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0470
   overall best weight:    0.2694

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
E 394 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.134676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.111614 restraints weight = 13341.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.38
r_work: 0.3281 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7925  Z= 0.152
  Angle     :  0.494   7.595  10747  Z= 0.256
  Chirality :  0.040   0.127   1132
  Planarity :  0.004   0.053   1385
  Dihedral  :  3.961  31.495   1099
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 18.34 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.39 (0.28), residues: 935
  helix:  1.38 (0.26), residues: 394
  sheet:  1.12 (0.40), residues: 177
  loop :  0.47 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.010   0.001   PHE H  99 
 TYR   0.018   0.001   TYR A 243 
 ARG   0.002   0.000   ARG A 219 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 170
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5170 (mmp) cc_final: 0.4679 (mmm)
REVERT: A  157 ASP cc_start: 0.6494 (p0) cc_final: 0.6134 (p0)
REVERT: A  183 TYR cc_start: 0.7251 (t80) cc_final: 0.6951 (t80)
REVERT: E  438 SER cc_start: 0.8325 (p) cc_final: 0.8104 (p)
REVERT: E  442 ASP cc_start: 0.8401 (m-30) cc_final: 0.8123 (m-30)
REVERT: E  443 SER cc_start: 0.8603 (m) cc_final: 0.8157 (p)
  outliers start: 10
  outliers final: 8
  residues processed: 174
  average time/residue: 0.2302
  time to fit residues: 52.4583
Evaluate side-chains
  171 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 163
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain E residue  500 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0980
   chunk 25 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 76 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 89 optimal weight:    0.2980
   chunk 52 optimal weight:    0.0570
   chunk 44 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.3498

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.108795 restraints weight = 20512.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 3.08
r_work: 0.3210 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7925  Z= 0.174
  Angle     :  0.499   7.111  10747  Z= 0.260
  Chirality :  0.040   0.129   1132
  Planarity :  0.004   0.049   1385
  Dihedral  :  3.926  30.063   1099
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.21 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.45 (0.28), residues: 935
  helix:  1.42 (0.26), residues: 394
  sheet:  1.11 (0.40), residues: 177
  loop :  0.55 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.012   0.001   PHE H  99 
 TYR   0.017   0.001   TYR A 243 
 ARG   0.002   0.000   ARG A 219 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 1.046 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5195 (mmp) cc_final: 0.4807 (mmm)
REVERT: E  442 ASP cc_start: 0.8374 (m-30) cc_final: 0.8139 (m-30)
REVERT: E  443 SER cc_start: 0.8582 (m) cc_final: 0.8163 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 168
  average time/residue: 0.2433
  time to fit residues: 53.7852
Evaluate side-chains
  165 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  500 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0270
   chunk 92 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 90 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 83 optimal weight:    0.2980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.131760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.108895 restraints weight = 13733.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.40
r_work: 0.3239 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   7925  Z= 0.223
  Angle     :  0.527   7.190  10747  Z= 0.275
  Chirality :  0.041   0.134   1132
  Planarity :  0.004   0.049   1385
  Dihedral  :  4.051  29.926   1099
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.46 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.38 (0.28), residues: 935
  helix:  1.39 (0.27), residues: 392
  sheet:  1.08 (0.39), residues: 176
  loop :  0.47 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.014   0.001   PHE H  99 
 TYR   0.017   0.002   TYR A 243 
 ARG   0.003   0.000   ARG A 219 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.862 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5322 (mmp) cc_final: 0.4950 (mmm)
REVERT: A  310 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7847 (mm-30)
REVERT: A  312 GLU cc_start: 0.8459 (tt0) cc_final: 0.7962 (tt0)
REVERT: E  442 ASP cc_start: 0.8568 (m-30) cc_final: 0.8299 (m-30)
REVERT: E  443 SER cc_start: 0.8615 (m) cc_final: 0.8188 (p)
  outliers start: 17
  outliers final: 12
  residues processed: 174
  average time/residue: 0.2280
  time to fit residues: 51.7419
Evaluate side-chains
  177 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 165
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain L residue   47 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    0.0050
   chunk 27 optimal weight:    0.3980
   chunk 92 optimal weight:    0.4980
   chunk 79 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.132531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.107754 restraints weight = 20848.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 3.14
r_work: 0.3193 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   7925  Z= 0.199
  Angle     :  0.514   6.661  10747  Z= 0.268
  Chirality :  0.041   0.131   1132
  Planarity :  0.004   0.048   1385
  Dihedral  :  3.984  28.667   1099
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.06 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.40 (0.28), residues: 935
  helix:  1.40 (0.27), residues: 394
  sheet:  1.05 (0.39), residues: 176
  loop :  0.51 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.012   0.001   PHE H  99 
 TYR   0.017   0.001   TYR A 279 
 ARG   0.002   0.000   ARG A 219 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5407 (mmp) cc_final: 0.5132 (mmm)
REVERT: E  442 ASP cc_start: 0.8566 (m-30) cc_final: 0.8254 (m-30)
REVERT: E  443 SER cc_start: 0.8554 (m) cc_final: 0.8121 (p)
REVERT: L    4 MET cc_start: 0.7996 (mmm) cc_final: 0.7530 (mmm)
REVERT: L   19 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7910 (m)
  outliers start: 13
  outliers final: 10
  residues processed: 171
  average time/residue: 0.2464
  time to fit residues: 54.8114
Evaluate side-chains
  173 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 68 optimal weight:    0.0010
   chunk 46 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0170
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.3224

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.132237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.109625 restraints weight = 13659.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.35
r_work: 0.3253 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090   7925  Z= 0.180
  Angle     :  0.512   6.354  10747  Z= 0.267
  Chirality :  0.041   0.130   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.891  27.052   1099
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.18 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.47 (0.28), residues: 935
  helix:  1.44 (0.27), residues: 394
  sheet:  1.26 (0.41), residues: 166
  loop :  0.50 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.010   0.001   PHE H  99 
 TYR   0.022   0.001   TYR A 279 
 ARG   0.004   0.000   ARG A 115 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5430 (mmp) cc_final: 0.5163 (mmm)
REVERT: E  443 SER cc_start: 0.8595 (m) cc_final: 0.8160 (p)
REVERT: L   19 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7951 (m)
  outliers start: 16
  outliers final: 11
  residues processed: 168
  average time/residue: 0.2328
  time to fit residues: 51.2173
Evaluate side-chains
  171 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0870
   chunk 20 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 64 optimal weight:    0.3980
   chunk 76 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 61 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 81 optimal weight:    0.4980
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.131714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.108750 restraints weight = 15538.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.53
r_work: 0.3229 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   7925  Z= 0.191
  Angle     :  0.528   6.540  10747  Z= 0.273
  Chirality :  0.041   0.132   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.907  25.586   1099
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.06 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.46 (0.28), residues: 935
  helix:  1.47 (0.27), residues: 392
  sheet:  1.23 (0.40), residues: 166
  loop :  0.47 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.011   0.001   PHE H  99 
 TYR   0.020   0.001   TYR A 279 
 ARG   0.003   0.000   ARG A 219 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5351 (mmp) cc_final: 0.5117 (mmm)
REVERT: E  443 SER cc_start: 0.8557 (m) cc_final: 0.8124 (p)
REVERT: L   19 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7913 (m)
  outliers start: 20
  outliers final: 13
  residues processed: 169
  average time/residue: 0.2376
  time to fit residues: 52.7248
Evaluate side-chains
  176 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 55 optimal weight:    0.1980
   chunk 28 optimal weight:    0.0270
   chunk 82 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 73 optimal weight:    0.1980
   overall best weight:    0.3838

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.131701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.107676 restraints weight = 19082.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.89
r_work: 0.3203 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093   7925  Z= 0.199
  Angle     :  0.539   7.011  10747  Z= 0.279
  Chirality :  0.041   0.138   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.926  24.687   1099
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 19.78 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.47 (0.28), residues: 935
  helix:  1.45 (0.27), residues: 392
  sheet:  1.22 (0.40), residues: 166
  loop :  0.49 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.011   0.001   PHE H  99 
 TYR   0.022   0.001   TYR A 279 
 ARG   0.004   0.000   ARG A 115 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5405 (mmp) cc_final: 0.5139 (mmm)
REVERT: A  310 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7599 (mm-30)
REVERT: A  312 GLU cc_start: 0.8268 (tt0) cc_final: 0.7678 (tt0)
REVERT: A  518 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7696 (mtp-110)
REVERT: E  443 SER cc_start: 0.8573 (m) cc_final: 0.8128 (p)
REVERT: L   19 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7905 (m)
  outliers start: 15
  outliers final: 13
  residues processed: 168
  average time/residue: 0.2404
  time to fit residues: 52.7681
Evaluate side-chains
  171 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0570
   chunk 46 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0770
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.3254

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 239 HIS
A 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.132158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.108031 restraints weight = 20690.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 3.02
r_work: 0.3199 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.121   7925  Z= 0.196
  Angle     :  0.533   7.183  10747  Z= 0.276
  Chirality :  0.041   0.136   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.842  23.756   1099
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 20.14 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.49 (0.28), residues: 935
  helix:  1.48 (0.27), residues: 392
  sheet:  1.26 (0.40), residues: 166
  loop :  0.49 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.010   0.001   PHE H  99 
 TYR   0.020   0.001   TYR A 243 
 ARG   0.003   0.000   ARG A 115 

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5349 (mmp) cc_final: 0.5115 (mmm)
REVERT: A  310 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7621 (mm-30)
REVERT: A  312 GLU cc_start: 0.8258 (tt0) cc_final: 0.7608 (tt0)
REVERT: E  443 SER cc_start: 0.8584 (m) cc_final: 0.8136 (p)
REVERT: L   19 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7907 (m)
  outliers start: 13
  outliers final: 12
  residues processed: 167
  average time/residue: 0.2483
  time to fit residues: 54.0881
Evaluate side-chains
  173 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 160
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   47 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 92 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0570
   chunk 30 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 35 optimal weight:    0.1980
   overall best weight:    0.3076

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.132443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.110174 restraints weight = 13165.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.29
r_work: 0.3262 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   7925  Z= 0.187
  Angle     :  0.533   7.051  10747  Z= 0.275
  Chirality :  0.041   0.135   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.834  22.942   1099
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.02 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.50 (0.28), residues: 935
  helix:  1.48 (0.27), residues: 392
  sheet:  1.27 (0.40), residues: 166
  loop :  0.50 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.020   0.001   TYR A 243 
 ARG   0.004   0.000   ARG A 115 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4937.68 seconds
wall clock time: 89 minutes 31.82 seconds (5371.82 seconds total)