Starting phenix.real_space_refine
on Wed Mar 12 10:14:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xxw_38763/03_2025/8xxw_38763.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xxw_38763/03_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_38763/03_2025/8xxw_38763.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xxw_38763/03_2025/8xxw_38763.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xxw_38763/03_2025/8xxw_38763.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xxw_38763/03_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-5624/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: 7.52, per 1000 atoms: 0.97
  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: 2.00
  Conformation dependent library (CDL) restraints added in 1.4 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: 0.89
  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: 2.18

  Time building geometry restraints manager: 2.36 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:             7.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     26.080
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.920
-------------------------------------------------------------------------------
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  : 1.031 
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: 0.2603
  time to fit residues: 53.3978
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  : 0.887 
-------------------------------------------------------------------------------
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 = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.111718 restraints weight = 10885.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.07
r_work: 0.3293 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    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 = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
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  : 0.767 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5210 (mmp) cc_final: 0.4552 (mmm)
REVERT: A  183 TYR cc_start: 0.7228 (t80) cc_final: 0.6874 (t80)
REVERT: E  443 SER cc_start: 0.8617 (m) cc_final: 0.8242 (p)
  outliers start: 8
  outliers final: 4
  residues processed: 168
  average time/residue: 0.3019
  time to fit residues: 65.9085
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  : 0.856 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0370
   chunk 91 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0000
   chunk 40 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0170
   overall best weight:    0.2500

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.134981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.111930 restraints weight = 13342.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.37
r_work: 0.3285 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    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 = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1129

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= 0.148
  Angle     :  0.491   7.550  10747  Z= 0.255
  Chirality :  0.040   0.127   1132
  Planarity :  0.004   0.053   1385
  Dihedral  :  3.947  31.353   1099
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 18.46 %
    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:  1.41 (0.28), residues: 935
  helix:  1.38 (0.26), residues: 394
  sheet:  1.24 (0.40), residues: 175
  loop :  0.43 (0.33), residues: 366

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 306 

*********************** 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
  178 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 169
  time to evaluate  : 0.792 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5175 (mmp) cc_final: 0.4684 (mmm)
REVERT: A  157 ASP cc_start: 0.6490 (p0) cc_final: 0.6128 (p0)
REVERT: A  183 TYR cc_start: 0.7248 (t80) cc_final: 0.6953 (t80)
REVERT: E  438 SER cc_start: 0.8323 (p) cc_final: 0.8102 (p)
REVERT: E  442 ASP cc_start: 0.8398 (m-30) cc_final: 0.8123 (m-30)
REVERT: E  443 SER cc_start: 0.8599 (m) cc_final: 0.8151 (p)
  outliers start: 9
  outliers final: 7
  residues processed: 173
  average time/residue: 0.2177
  time to fit residues: 49.7095
Evaluate side-chains
  167 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 160
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  233 ILE
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  449 THR
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:    0.0970
   chunk 25 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0980
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.132625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.108036 restraints weight = 20498.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 3.06
r_work: 0.3199 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
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   0.061   7925  Z= 0.195
  Angle     :  0.511   7.291  10747  Z= 0.266
  Chirality :  0.041   0.130   1132
  Planarity :  0.004   0.050   1385
  Dihedral  :  3.992  30.646   1099
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.34 %
    Favored  : 79.73 %
  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:  1.41 (0.28), residues: 935
  helix:  1.37 (0.26), residues: 394
  sheet:  1.09 (0.40), residues: 177
  loop :  0.54 (0.33), residues: 364

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   0.014   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
  180 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5164 (mmp) cc_final: 0.4765 (mmm)
REVERT: E  442 ASP cc_start: 0.8389 (m-30) cc_final: 0.8163 (m-30)
REVERT: E  443 SER cc_start: 0.8586 (m) cc_final: 0.8167 (p)
  outliers start: 16
  outliers final: 11
  residues processed: 169
  average time/residue: 0.2213
  time to fit residues: 49.1369
Evaluate side-chains
  168 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 157
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0050
   chunk 92 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 90 optimal weight:    0.3980
   chunk 80 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0170
   overall best weight:    0.3434

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.133547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.110417 restraints weight = 13752.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.43
r_work: 0.3259 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3256
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3256
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1393

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= 0.178
  Angle     :  0.502   6.703  10747  Z= 0.261
  Chirality :  0.040   0.129   1132
  Planarity :  0.004   0.048   1385
  Dihedral  :  3.915  29.066   1099
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.09 %
    Favored  : 79.73 %
  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:  1.42 (0.27), residues: 394
  sheet:  1.07 (0.40), residues: 177
  loop :  0.59 (0.33), residues: 364

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   0.011   0.001   PHE H  99 
 TYR   0.017   0.001   TYR A 243 
 ARG   0.002   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: 18
    poor density    : 165
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5103 (mmp) cc_final: 0.4748 (mmm)
REVERT: A  310 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7581 (mm-30)
REVERT: A  312 GLU cc_start: 0.8214 (tt0) cc_final: 0.7706 (tt0)
REVERT: E  442 ASP cc_start: 0.8481 (m-30) cc_final: 0.8212 (m-30)
REVERT: E  443 SER cc_start: 0.8537 (m) cc_final: 0.8123 (p)
  outliers start: 18
  outliers final: 12
  residues processed: 173
  average time/residue: 0.2213
  time to fit residues: 50.2420
Evaluate side-chains
  176 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 164
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
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  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  500 THR
Chi-restraints excluded: chain L residue   10 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    0.0670
   chunk 27 optimal weight:    0.0980
   chunk 92 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 80 optimal weight:    0.2980
   chunk 62 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 56 optimal weight:    0.3980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.2918

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.134088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.109209 restraints weight = 20886.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 3.14
r_work: 0.3218 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    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 = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   7925  Z= 0.166
  Angle     :  0.492   6.265  10747  Z= 0.257
  Chirality :  0.040   0.129   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.834  27.012   1099
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 18.94 %
    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:  1.55 (0.28), residues: 935
  helix:  1.48 (0.27), residues: 394
  sheet:  1.32 (0.41), residues: 166
  loop :  0.55 (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   0.018   0.001   TYR A 243 
 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
  175 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5177 (mmp) cc_final: 0.4912 (mmm)
REVERT: E  442 ASP cc_start: 0.8551 (m-30) cc_final: 0.8207 (m-30)
REVERT: E  443 SER cc_start: 0.8548 (m) cc_final: 0.8124 (p)
REVERT: L    4 MET cc_start: 0.7973 (mmm) cc_final: 0.7569 (mmm)
  outliers start: 14
  outliers final: 12
  residues processed: 167
  average time/residue: 0.2292
  time to fit residues: 50.3052
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  : 0.818 
-------------------------------------------------------------------------------
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  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  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    0.0970
   chunk 68 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 71 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.130320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.107771 restraints weight = 13662.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.33
r_work: 0.3229 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    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 = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   7925  Z= 0.239
  Angle     :  0.553  11.461  10747  Z= 0.285
  Chirality :  0.042   0.141   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  4.042  27.370   1099
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.18 %
    Favored  : 78.77 %
  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: 394
  sheet:  1.00 (0.39), residues: 176
  loop :  0.52 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.014   0.001   PHE H  99 
 TYR   0.019   0.002   TYR A 279 
 ARG   0.003   0.000   ARG A 219 

*********************** 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
  184 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 167
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5532 (mmp) cc_final: 0.5218 (mmm)
REVERT: A  310 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7796 (mm-30)
REVERT: A  312 GLU cc_start: 0.8424 (tt0) cc_final: 0.7929 (tt0)
REVERT: E  442 ASP cc_start: 0.8616 (m-30) cc_final: 0.8312 (m-30)
REVERT: E  443 SER cc_start: 0.8604 (m) cc_final: 0.8187 (p)
REVERT: L   19 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7999 (m)
  outliers start: 17
  outliers final: 13
  residues processed: 177
  average time/residue: 0.2233
  time to fit residues: 51.7423
Evaluate side-chains
  174 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
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  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 L residue    7 SER
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:    0.2980
   chunk 70 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0010
   chunk 20 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.3386

-------------------------------------------------------------------------------
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 = 0.131825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.108777 restraints weight = 15657.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.55
r_work: 0.3230 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3232
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3232
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092   7925  Z= 0.186
  Angle     :  0.530  10.274  10747  Z= 0.273
  Chirality :  0.041   0.130   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.924  26.471   1099
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.94 %
    Favored  : 78.65 %
  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:  1.44 (0.28), residues: 935
  helix:  1.46 (0.27), residues: 392
  sheet:  1.02 (0.39), residues: 176
  loop :  0.53 (0.34), residues: 367

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 279 
 ARG   0.006   0.000   ARG A 115 

*********************** 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
  184 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5300 (mmp) cc_final: 0.5043 (mmm)
REVERT: A  310 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7547 (mm-30)
REVERT: A  312 GLU cc_start: 0.8235 (tt0) cc_final: 0.7703 (tt0)
REVERT: E  442 ASP cc_start: 0.8523 (m-30) cc_final: 0.8181 (m-30)
REVERT: E  443 SER cc_start: 0.8551 (m) cc_final: 0.8118 (p)
REVERT: L   19 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7899 (m)
  outliers start: 20
  outliers final: 12
  residues processed: 176
  average time/residue: 0.2426
  time to fit residues: 56.2072
Evaluate side-chains
  167 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  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  500 THR
Chi-restraints excluded: chain H residue   11 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0270
   chunk 28 optimal weight:    0.0670
   chunk 82 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0570
   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
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.132721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.108778 restraints weight = 19208.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.90
r_work: 0.3217 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.113   7925  Z= 0.180
  Angle     :  0.529   9.859  10747  Z= 0.273
  Chirality :  0.040   0.143   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.851  24.287   1099
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.42 %
    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:  1.54 (0.28), residues: 935
  helix:  1.53 (0.27), residues: 392
  sheet:  1.26 (0.40), residues: 166
  loop :  0.52 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 477 
 HIS   0.002   0.001   HIS A 401 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.019   0.001   TYR A 243 
 ARG   0.002   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
  172 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 158
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5315 (mmp) cc_final: 0.5076 (mmm)
REVERT: A  310 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7615 (mm-30)
REVERT: A  312 GLU cc_start: 0.8239 (tt0) cc_final: 0.7727 (tt0)
REVERT: A  518 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7738 (mtp-110)
REVERT: E  442 ASP cc_start: 0.8529 (m-30) cc_final: 0.8185 (m-30)
REVERT: E  443 SER cc_start: 0.8559 (m) cc_final: 0.8121 (p)
REVERT: L    4 MET cc_start: 0.8106 (mmm) cc_final: 0.7567 (tpt)
REVERT: L   19 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7879 (m)
  outliers start: 14
  outliers final: 11
  residues processed: 167
  average time/residue: 0.1963
  time to fit residues: 44.2287
Evaluate side-chains
  169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 157
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
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  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   11 LEU
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 13 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 74 optimal weight:    0.2980
   chunk 89 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9990
   chunk 90 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.4338

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.131691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.107231 restraints weight = 20796.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 3.07
r_work: 0.3188 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.104   7925  Z= 0.217
  Angle     :  0.554  10.012  10747  Z= 0.287
  Chirality :  0.041   0.137   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.918  24.143   1099
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 19.30 %
    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:  1.46 (0.28), residues: 935
  helix:  1.46 (0.27), residues: 392
  sheet:  1.21 (0.40), residues: 166
  loop :  0.47 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.012   0.001   PHE H  99 
 TYR   0.024   0.001   TYR A  50 
 ARG   0.003   0.000   ARG A 219 

********************** 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
  169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A   50 TYR cc_start: 0.8580 (t80) cc_final: 0.8380 (t80)
REVERT: A  123 MET cc_start: 0.5443 (mmp) cc_final: 0.5180 (mmm)
REVERT: A  310 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7626 (mm-30)
REVERT: A  312 GLU cc_start: 0.8271 (tt0) cc_final: 0.7847 (tt0)
REVERT: E  443 SER cc_start: 0.8574 (m) cc_final: 0.8134 (p)
REVERT: L   19 VAL cc_start: 0.8206 (OUTLIER) cc_final: 0.7921 (m)
  outliers start: 15
  outliers final: 13
  residues processed: 161
  average time/residue: 0.2159
  time to fit residues: 46.4240
Evaluate side-chains
  167 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  244 VAL
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   11 LEU
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:    0.2980
   chunk 92 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0770
   chunk 31 optimal weight:    0.9980
   chunk 51 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.131156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.108876 restraints weight = 13252.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.30
r_work: 0.3242 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.099   7925  Z= 0.226
  Angle     :  0.560  10.052  10747  Z= 0.290
  Chirality :  0.042   0.139   1132
  Planarity :  0.004   0.047   1385
  Dihedral  :  3.941  24.214   1099
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.30 %
    Favored  : 78.77 %
  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:  1.42 (0.28), residues: 935
  helix:  1.43 (0.27), residues: 392
  sheet:  1.21 (0.40), residues: 166
  loop :  0.44 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.013   0.001   PHE H  99 
 TYR   0.019   0.001   TYR A 243 
 ARG   0.003   0.000   ARG A 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5065.93 seconds
wall clock time: 89 minutes 46.15 seconds (5386.15 seconds total)