Starting phenix.real_space_refine
on Sun Jul 27 00:42:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y95_39070/07_2025/8y95_39070.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y95_39070/07_2025/8y95_39070.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y95_39070/07_2025/8y95_39070.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y95_39070/07_2025/8y95_39070.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y95_39070/07_2025/8y95_39070.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y95_39070/07_2025/8y95_39070.cif"
  }
  resolution = 3.24
  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=   0.050
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: 6
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      2      4.86       5
     Na      2      4.78       5
     C    6042      2.51       5
     N    1406      2.21       5
     O    1526      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9018
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 562, 4495
          Classifications: {'peptide': 562}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 542}
    Chain: "D"
      Number of atoms: 4495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 562, 4495
          Classifications: {'peptide': 562}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 542}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 14
          Unusual residues: {' CL': 1, ' NA': 1, 'E5E': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 14
          Unusual residues: {' CL': 1, ' NA': 1, 'E5E': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.09, per 1000 atoms: 0.68
  Number of scatterers: 9018
  At special positions: 0
  Unit cell: (100.01, 107.31, 93.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      2     17.00
     S      40     16.00
     Na      2     11.00
     O    1526      8.00
     N    1406      7.00
     C    6042      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 0 sheets defined
      77.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 74
      removed outlier: 4.005A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 3.713A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 91 through 107
      Proline residue:  A  97  - end of helix
      removed outlier: 3.530A  pdb=" N   ILE A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 121
      removed outlier: 3.581A  pdb=" N   TYR A 111 " --> pdb=" O   MET A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 134
    Processing helix  chain 'A' and resid 135 through 166
      removed outlier: 3.763A  pdb=" N   ILE A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 143 " --> pdb=" O   TYR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 175
      removed outlier: 3.892A  pdb=" N   ASP A 175 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 262 through 267
      removed outlier: 3.714A  pdb=" N   THR A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 282
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 4.020A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA A 293 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 302
    Processing helix  chain 'A' and resid 304 through 320
      removed outlier: 3.950A  pdb=" N   TRP A 308 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 332
    Processing helix  chain 'A' and resid 338 through 373
      removed outlier: 3.510A  pdb=" N   ASP A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 398
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.574A  pdb=" N   TRP A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 441
      removed outlier: 3.636A  pdb=" N   LYS A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ARG A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   HIS A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 435 through 441'
    Processing helix  chain 'A' and resid 441 through 461
      removed outlier: 4.237A  pdb=" N   PHE A 447 " --> pdb=" O   LYS A 443 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 494
      removed outlier: 3.627A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   THR A 470 " --> pdb=" O   ILE A 466 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LEU A 471 " --> pdb=" O   TYR A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 510
      removed outlier: 3.683A  pdb=" N   PHE A 501 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 580
      removed outlier: 3.830A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      Proline residue:  A 570  - end of helix
    Processing helix  chain 'A' and resid 583 through 592
    Processing helix  chain 'A' and resid 598 through 603
      removed outlier: 3.771A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 616
      removed outlier: 4.047A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 74
      removed outlier: 4.010A  pdb=" N   PHE D  65 " --> pdb=" O   LYS D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 89
      removed outlier: 3.710A  pdb=" N   VAL D  79 " --> pdb=" O   ASP D  75 " (cutoff:3.500A)
      Proline residue:  D  83  - end of helix
    Processing helix  chain 'D' and resid 91 through 107
      Proline residue:  D  97  - end of helix
      removed outlier: 3.528A  pdb=" N   ILE D 104 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 121
      removed outlier: 3.581A  pdb=" N   TYR D 111 " --> pdb=" O   MET D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 134
    Processing helix  chain 'D' and resid 135 through 166
      removed outlier: 3.778A  pdb=" N   ILE D 142 " --> pdb=" O   GLY D 138 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU D 143 " --> pdb=" O   TYR D 139 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 175
      removed outlier: 3.890A  pdb=" N   ASP D 175 " --> pdb=" O   PRO D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 216
    Processing helix  chain 'D' and resid 220 through 224
    Processing helix  chain 'D' and resid 234 through 253
    Processing helix  chain 'D' and resid 262 through 267
      removed outlier: 3.718A  pdb=" N   THR D 266 " --> pdb=" O   VAL D 262 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 268 through 282
    Processing helix  chain 'D' and resid 286 through 295
      removed outlier: 4.021A  pdb=" N   GLY D 290 " --> pdb=" O   GLY D 286 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA D 293 " --> pdb=" O   ASN D 289 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 302
    Processing helix  chain 'D' and resid 304 through 320
      removed outlier: 3.951A  pdb=" N   TRP D 308 " --> pdb=" O   GLU D 304 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY D 320 " --> pdb=" O   PHE D 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 332
    Processing helix  chain 'D' and resid 338 through 373
      removed outlier: 3.508A  pdb=" N   ASP D 342 " --> pdb=" O   ASN D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 386 through 398
      Proline residue:  D 392  - end of helix
    Processing helix  chain 'D' and resid 400 through 435
      removed outlier: 3.572A  pdb=" N   TRP D 404 " --> pdb=" O   GLY D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 435 through 441
      removed outlier: 3.635A  pdb=" N   LYS D 439 " --> pdb=" O   PHE D 435 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ARG D 440 " --> pdb=" O   GLN D 436 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   HIS D 441 " --> pdb=" O   VAL D 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 435 through 441'
    Processing helix  chain 'D' and resid 441 through 461
      removed outlier: 4.250A  pdb=" N   PHE D 447 " --> pdb=" O   LYS D 443 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLY D 448 " --> pdb=" O   LEU D 444 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 464 through 494
      removed outlier: 3.624A  pdb=" N   VAL D 468 " --> pdb=" O   GLY D 464 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   THR D 470 " --> pdb=" O   ILE D 466 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU D 471 " --> pdb=" O   TYR D 467 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 497 through 510
      removed outlier: 3.676A  pdb=" N   PHE D 501 " --> pdb=" O   GLY D 497 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 514 through 523
    Processing helix  chain 'D' and resid 523 through 539
    Processing helix  chain 'D' and resid 551 through 580
      removed outlier: 3.831A  pdb=" N   ASN D 555 " --> pdb=" O   PRO D 551 " (cutoff:3.500A)
      Proline residue:  D 570  - end of helix
    Processing helix  chain 'D' and resid 583 through 592
    Processing helix  chain 'D' and resid 598 through 603
      removed outlier: 3.772A  pdb=" N   ALA D 602 " --> pdb=" O   HIS D 598 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 610 through 616
      removed outlier: 4.046A  pdb=" N   TRP D 614 " --> pdb=" O   GLN D 610 " (cutoff:3.500A)

    572 hydrogen bonds defined for protein.
    1680 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: 2.67

  Time building geometry restraints manager: 3.07 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: 2646
        1.34 -     1.46: 2361
        1.46 -     1.58: 4237
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 9306
  Sorted by residual:
  bond pdb=" CAJ E5E D 701 "
       pdb=" OAC E5E D 701 "
    ideal  model  delta    sigma   weight residual
    1.350  1.401 -0.051 2.00e-02 2.50e+03 6.51e+00
  bond pdb=" CAJ E5E A 701 "
       pdb=" OAC E5E A 701 "
    ideal  model  delta    sigma   weight residual
    1.350  1.394 -0.044 2.00e-02 2.50e+03 4.93e+00
  bond pdb=" CAI E5E A 701 "
       pdb=" OAB E5E A 701 "
    ideal  model  delta    sigma   weight residual
    1.354  1.395 -0.041 2.00e-02 2.50e+03 4.26e+00
  bond pdb=" CAI E5E D 701 "
       pdb=" OAB E5E D 701 "
    ideal  model  delta    sigma   weight residual
    1.354  1.394 -0.040 2.00e-02 2.50e+03 4.08e+00
  bond pdb=" CAI E5E A 701 "
       pdb=" CAJ E5E A 701 "
    ideal  model  delta    sigma   weight residual
    1.401  1.364  0.037 2.00e-02 2.50e+03 3.48e+00
  ... (remaining 9301 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 12455
        1.72 -     3.43: 194
        3.43 -     5.15: 34
        5.15 -     6.87: 11
        6.87 -     8.59: 2
  Bond angle restraints: 12696
  Sorted by residual:
  angle pdb=" C   ASP A 546 "
        pdb=" CA  ASP A 546 "
        pdb=" CB  ASP A 546 "
      ideal   model   delta    sigma   weight residual
     110.92  115.72   -4.80 1.59e+00 3.96e-01 9.11e+00
  angle pdb=" C   ASP D 546 "
        pdb=" CA  ASP D 546 "
        pdb=" CB  ASP D 546 "
      ideal   model   delta    sigma   weight residual
     110.92  115.68   -4.76 1.59e+00 3.96e-01 8.98e+00
  angle pdb=" N   GLY D 231 "
        pdb=" CA  GLY D 231 "
        pdb=" C   GLY D 231 "
      ideal   model   delta    sigma   weight residual
     111.21  114.29   -3.08 1.04e+00 9.25e-01 8.75e+00
  angle pdb=" N   GLY A 231 "
        pdb=" CA  GLY A 231 "
        pdb=" C   GLY A 231 "
      ideal   model   delta    sigma   weight residual
     111.21  114.27   -3.06 1.04e+00 9.25e-01 8.65e+00
  angle pdb=" C   GLY D 106 "
        pdb=" N   MET D 107 "
        pdb=" CA  MET D 107 "
      ideal   model   delta    sigma   weight residual
     121.80  114.95    6.85 2.44e+00 1.68e-01 7.89e+00
  ... (remaining 12691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4918
       17.89 -    35.77: 210
       35.77 -    53.66: 56
       53.66 -    71.55: 6
       71.55 -    89.43: 6
  Dihedral angle restraints: 5196
    sinusoidal: 1950
      harmonic: 3246
  Sorted by residual:
  dihedral pdb=" CA  THR D 268 "
           pdb=" C   THR D 268 "
           pdb=" N   LEU D 269 "
           pdb=" CA  LEU D 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.60  -19.40     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  THR A 268 "
           pdb=" C   THR A 268 "
           pdb=" N   LEU A 269 "
           pdb=" CA  LEU A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.76  -19.24     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  SER A 493 "
           pdb=" C   SER A 493 "
           pdb=" N   TRP A 494 "
           pdb=" CA  TRP A 494 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.36  -15.64     0      5.00e+00 4.00e-02 9.78e+00
  ... (remaining 5193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1046
       0.036 -    0.072: 304
       0.072 -    0.108: 52
       0.108 -    0.145: 9
       0.145 -    0.181: 3
  Chirality restraints: 1414
  Sorted by residual:
  chirality pdb=" CAL E5E D 701 "
            pdb=" CAH E5E D 701 "
            pdb=" CAK E5E D 701 "
            pdb=" OAD E5E D 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -2.49    0.18 2.00e-01 2.50e+01 8.16e-01
  chirality pdb=" CA  LEU A 269 "
            pdb=" N   LEU A 269 "
            pdb=" C   LEU A 269 "
            pdb=" CB  LEU A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  LEU D 269 "
            pdb=" N   LEU D 269 "
            pdb=" C   LEU D 269 "
            pdb=" CB  LEU D 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.48e-01
  ... (remaining 1411 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 477 "    0.015 2.00e-02 2.50e+03   2.95e-02 8.73e+00
        pdb=" C   ALA A 477 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ALA A 477 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLY A 478 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 477 "   -0.015 2.00e-02 2.50e+03   2.95e-02 8.69e+00
        pdb=" C   ALA D 477 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ALA D 477 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLY D 478 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 481 "   -0.014 2.00e-02 2.50e+03   2.75e-02 7.55e+00
        pdb=" C   ILE D 481 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ILE D 481 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LEU D 482 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        1.40 -     2.10: 2
        2.10 -     2.80: 2584
        2.80 -     3.50: 13256
        3.50 -     4.20: 21664
        4.20 -     4.90: 39302
  Nonbonded interactions: 76808
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  78 "
            pdb="NA    NA A 703 "
     model   vdw
     1.402 2.470
  nonbonded pdb=" OD1 ASN A 350 "
            pdb="NA    NA A 703 "
     model   vdw
     2.088 2.470
  nonbonded pdb=" OH  TYR D  98 "
            pdb="CL    CL D 702 "
     model   vdw
     2.113 3.190
  nonbonded pdb=" OH  TYR A  98 "
            pdb="CL    CL A 702 "
     model   vdw
     2.161 3.190
  nonbonded pdb=" OH  TYR A 496 "
            pdb=" OD2 ASP A 504 "
     model   vdw
     2.216 3.040
  ... (remaining 76803 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.590
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.040
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6251
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      :  0.014   0.810   9309  Z= 1.379
  Angle     :  0.589   8.585  12696  Z= 0.342
  Chirality :  0.036   0.181   1414
  Planarity :  0.006   0.060   1544
  Dihedral  : 11.301  89.435   3132
  Min Nonbonded Distance : 1.402

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  :  6.75 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.89 (0.23), residues: 1120
  helix: -0.91 (0.18), residues: 760
  sheet:  None (None), residues: 0
  loop : -1.73 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 553 
 HIS   0.002   0.000   HIS D 228 
 PHE   0.014   0.001   PHE D  65 
 TYR   0.024   0.001   TYR D 151 
 ARG   0.002   0.000   ARG D 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16661 (  572)
  hydrogen bonds       : angle       6.83494 ( 1680)
  covalent geometry    : bond        0.00253 ( 9306)
  covalent geometry    : angle       0.58886 (12696)
  Misc. bond           : bond        0.76347 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 278
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8294 (m-10)
REVERT: A  303 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7796 (mmtt)
REVERT: A  377 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6497 (mm-30)
REVERT: A  519 LEU cc_start: 0.8096 (mt) cc_final: 0.7734 (mt)
REVERT: A  544 THR cc_start: 0.7115 (t) cc_final: 0.6758 (t)
REVERT: A  548 TYR cc_start: 0.7364 (t80) cc_final: 0.6795 (t80)
REVERT: A  563 LEU cc_start: 0.7006 (mt) cc_final: 0.6767 (mt)
REVERT: A  615 LEU cc_start: 0.8194 (tt) cc_final: 0.7948 (mt)
REVERT: D  107 MET cc_start: 0.4599 (OUTLIER) cc_final: 0.3819 (mpp)
REVERT: D  120 ASN cc_start: 0.8215 (m-40) cc_final: 0.7924 (m110)
REVERT: D  133 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8295 (m-10)
REVERT: D  303 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7778 (mmtt)
REVERT: D  377 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6568 (mm-30)
REVERT: D  515 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7112 (tp)
REVERT: D  519 LEU cc_start: 0.8130 (mt) cc_final: 0.7787 (mt)
REVERT: D  544 THR cc_start: 0.7061 (t) cc_final: 0.6708 (t)
REVERT: D  548 TYR cc_start: 0.7356 (t80) cc_final: 0.6860 (t80)
REVERT: D  563 LEU cc_start: 0.7028 (mt) cc_final: 0.6783 (mt)
REVERT: D  615 LEU cc_start: 0.8209 (tt) cc_final: 0.7971 (mt)
  outliers start: 42
  outliers final: 6
  residues processed: 309
  average time/residue: 0.2061
  time to fit residues: 88.8334
Evaluate side-chains
  172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 162
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain D residue  107 MET
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  469 LEU
Chi-restraints excluded: chain D residue  473 ASP
Chi-restraints excluded: chain D residue  515 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 53 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 101 optimal weight:    5.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
A  89 ASN
A 184 ASN
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 GLN
A 599 HIS
A 610 GLN
D  89 ASN
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 184 ASN
D 333 ASN
D 350 ASN
D 599 HIS
D 610 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.193294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.165676 restraints weight = 12137.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.4008 rms_B_bonded: 2.48
r_work: 0.3879 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9309  Z= 0.156
  Angle     :  0.596   7.487  12696  Z= 0.308
  Chirality :  0.040   0.170   1414
  Planarity :  0.005   0.057   1544
  Dihedral  :  5.821  50.331   1245
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 13.19 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1120
  helix:  0.34 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -0.97 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  80 
 HIS   0.014   0.001   HIS A 598 
 PHE   0.036   0.002   PHE A 359 
 TYR   0.020   0.002   TYR A 152 
 ARG   0.006   0.001   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05118 (  572)
  hydrogen bonds       : angle       4.94290 ( 1680)
  covalent geometry    : bond        0.00337 ( 9306)
  covalent geometry    : angle       0.59565 (12696)
  Misc. bond           : bond        0.00609 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 182
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7545 (mp0)
REVERT: A  133 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8466 (m-80)
REVERT: A  189 LYS cc_start: 0.7324 (ttpt) cc_final: 0.6622 (tptt)
REVERT: A  303 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7747 (mmtt)
REVERT: A  367 TYR cc_start: 0.7738 (t80) cc_final: 0.7422 (t80)
REVERT: A  377 GLU cc_start: 0.7644 (mt-10) cc_final: 0.6817 (mm-30)
REVERT: A  519 LEU cc_start: 0.8420 (mt) cc_final: 0.8188 (mt)
REVERT: A  548 TYR cc_start: 0.7857 (t80) cc_final: 0.6916 (t80)
REVERT: A  563 LEU cc_start: 0.7388 (mt) cc_final: 0.7140 (mt)
REVERT: A  615 LEU cc_start: 0.8111 (tt) cc_final: 0.7831 (mt)
REVERT: D  107 MET cc_start: 0.5740 (mpp) cc_final: 0.5341 (mmp)
REVERT: D  122 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7542 (mp0)
REVERT: D  133 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8498 (m-80)
REVERT: D  303 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7724 (mmtt)
REVERT: D  332 TYR cc_start: 0.7796 (m-80) cc_final: 0.7530 (m-80)
REVERT: D  367 TYR cc_start: 0.7690 (t80) cc_final: 0.7366 (t80)
REVERT: D  377 GLU cc_start: 0.7626 (mt-10) cc_final: 0.6821 (mm-30)
REVERT: D  519 LEU cc_start: 0.8543 (mt) cc_final: 0.8275 (mt)
REVERT: D  548 TYR cc_start: 0.7822 (t80) cc_final: 0.6914 (t80)
REVERT: D  563 LEU cc_start: 0.7442 (mt) cc_final: 0.7165 (mt)
REVERT: D  615 LEU cc_start: 0.8121 (tt) cc_final: 0.7850 (mt)
  outliers start: 43
  outliers final: 24
  residues processed: 217
  average time/residue: 0.1692
  time to fit residues: 54.2313
Evaluate side-chains
  192 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 166
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  205 TYR
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  313 THR
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  534 VAL
Chi-restraints excluded: chain D residue  579 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 32 optimal weight:    0.0570
   chunk 16 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0980
   overall best weight:    0.5300

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 HIS
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 610 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.189172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.159682 restraints weight = 12265.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 2.53
r_work: 0.3817 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.3358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9309  Z= 0.130
  Angle     :  0.546   7.736  12696  Z= 0.278
  Chirality :  0.038   0.152   1414
  Planarity :  0.004   0.048   1544
  Dihedral  :  5.256  48.681   1234
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.09 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1120
  helix:  0.74 (0.19), residues: 770
  sheet:  None (None), residues: 0
  loop : -0.69 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 517 
 HIS   0.007   0.001   HIS D 598 
 PHE   0.015   0.001   PHE D  65 
 TYR   0.018   0.001   TYR A 151 
 ARG   0.004   0.000   ARG D 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04697 (  572)
  hydrogen bonds       : angle       4.87428 ( 1680)
  covalent geometry    : bond        0.00277 ( 9306)
  covalent geometry    : angle       0.54606 (12696)
  Misc. bond           : bond        0.00518 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: A   88 LYS cc_start: 0.8557 (pttt) cc_final: 0.8321 (ptpt)
REVERT: A  122 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7628 (mp0)
REVERT: A  133 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8493 (m-80)
REVERT: A  189 LYS cc_start: 0.7348 (ttpt) cc_final: 0.6607 (tptt)
REVERT: A  303 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7705 (mmtt)
REVERT: A  367 TYR cc_start: 0.7909 (t80) cc_final: 0.7553 (t80)
REVERT: A  377 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6823 (mm-30)
REVERT: A  563 LEU cc_start: 0.7541 (mt) cc_final: 0.7250 (mt)
REVERT: A  615 LEU cc_start: 0.8087 (tt) cc_final: 0.7836 (mt)
REVERT: D  120 ASN cc_start: 0.8406 (m-40) cc_final: 0.7309 (m110)
REVERT: D  122 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7603 (mp0)
REVERT: D  133 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8507 (m-80)
REVERT: D  303 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7667 (mmtt)
REVERT: D  367 TYR cc_start: 0.7811 (t80) cc_final: 0.7456 (t80)
REVERT: D  377 GLU cc_start: 0.7740 (mt-10) cc_final: 0.6894 (mm-30)
REVERT: D  434 ASP cc_start: 0.8055 (t0) cc_final: 0.7855 (t0)
REVERT: D  563 LEU cc_start: 0.7555 (mt) cc_final: 0.7249 (mt)
REVERT: D  584 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6915 (tt)
REVERT: D  615 LEU cc_start: 0.8076 (tt) cc_final: 0.7841 (mt)
  outliers start: 32
  outliers final: 23
  residues processed: 189
  average time/residue: 0.1889
  time to fit residues: 52.3612
Evaluate side-chains
  176 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  205 TYR
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  584 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 73 optimal weight:    0.4980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 184 ASN
D 610 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.182585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.151415 restraints weight = 12198.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 2.53
r_work: 0.3720 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9309  Z= 0.142
  Angle     :  0.561   7.613  12696  Z= 0.284
  Chirality :  0.038   0.171   1414
  Planarity :  0.004   0.042   1544
  Dihedral  :  5.163  47.268   1234
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.19 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.25), residues: 1120
  helix:  0.91 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop : -0.64 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 517 
 HIS   0.004   0.001   HIS D 598 
 PHE   0.016   0.001   PHE D  65 
 TYR   0.015   0.001   TYR D 151 
 ARG   0.005   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04872 (  572)
  hydrogen bonds       : angle       4.92227 ( 1680)
  covalent geometry    : bond        0.00307 ( 9306)
  covalent geometry    : angle       0.56085 (12696)
  Misc. bond           : bond        0.00458 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ASN cc_start: 0.8492 (m-40) cc_final: 0.7278 (m110)
REVERT: A  122 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7584 (mp0)
REVERT: A  133 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8484 (m-80)
REVERT: A  189 LYS cc_start: 0.7333 (ttpt) cc_final: 0.6540 (tptt)
REVERT: A  303 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7683 (mmtt)
REVERT: A  367 TYR cc_start: 0.7981 (t80) cc_final: 0.7558 (t80)
REVERT: A  377 GLU cc_start: 0.7770 (mt-10) cc_final: 0.6864 (mm-30)
REVERT: A  473 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.5533 (t0)
REVERT: A  508 MET cc_start: 0.8608 (mtp) cc_final: 0.8308 (mtp)
REVERT: A  563 LEU cc_start: 0.7812 (mt) cc_final: 0.7570 (mt)
REVERT: A  586 GLU cc_start: 0.7105 (tt0) cc_final: 0.6869 (tt0)
REVERT: A  615 LEU cc_start: 0.8076 (tt) cc_final: 0.7828 (mt)
REVERT: D  133 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8555 (m-80)
REVERT: D  303 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7674 (mmtt)
REVERT: D  367 TYR cc_start: 0.7959 (t80) cc_final: 0.7530 (t80)
REVERT: D  377 GLU cc_start: 0.7842 (mt-10) cc_final: 0.6918 (mm-30)
REVERT: D  473 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.4347 (t0)
REVERT: D  519 LEU cc_start: 0.8605 (mt) cc_final: 0.8385 (mt)
REVERT: D  563 LEU cc_start: 0.7840 (mt) cc_final: 0.7604 (mt)
REVERT: D  584 LEU cc_start: 0.7525 (mm) cc_final: 0.6920 (tt)
REVERT: D  586 GLU cc_start: 0.7083 (tt0) cc_final: 0.6857 (tt0)
REVERT: D  615 LEU cc_start: 0.8061 (tt) cc_final: 0.7795 (mt)
  outliers start: 33
  outliers final: 23
  residues processed: 189
  average time/residue: 0.1762
  time to fit residues: 48.1337
Evaluate side-chains
  177 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  205 TYR
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  473 ASP
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  579 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 HIS
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 280 HIS
D 610 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.173192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.140457 restraints weight = 12281.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.52
r_work: 0.3602 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9309  Z= 0.180
  Angle     :  0.603   8.761  12696  Z= 0.309
  Chirality :  0.040   0.173   1414
  Planarity :  0.004   0.040   1544
  Dihedral  :  5.227  48.022   1230
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 16.56 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.25), residues: 1120
  helix:  0.84 (0.19), residues: 762
  sheet:  None (None), residues: 0
  loop : -0.42 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 517 
 HIS   0.005   0.001   HIS A 222 
 PHE   0.018   0.002   PHE D 409 
 TYR   0.018   0.002   TYR A 572 
 ARG   0.003   0.000   ARG A 587 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05611 (  572)
  hydrogen bonds       : angle       5.14111 ( 1680)
  covalent geometry    : bond        0.00408 ( 9306)
  covalent geometry    : angle       0.60252 (12696)
  Misc. bond           : bond        0.00536 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 160
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8627 (m-80)
REVERT: A  189 LYS cc_start: 0.7302 (ttpt) cc_final: 0.6517 (tptt)
REVERT: A  303 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7718 (mmtt)
REVERT: A  377 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7060 (mm-30)
REVERT: A  473 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6134 (t0)
REVERT: A  586 GLU cc_start: 0.7145 (tt0) cc_final: 0.6904 (tt0)
REVERT: A  615 LEU cc_start: 0.8125 (tt) cc_final: 0.7817 (mt)
REVERT: D  122 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7579 (mp0)
REVERT: D  133 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8625 (m-80)
REVERT: D  303 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7711 (mmtt)
REVERT: D  377 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7096 (mm-30)
REVERT: D  540 PHE cc_start: 0.8934 (t80) cc_final: 0.8694 (t80)
REVERT: D  584 LEU cc_start: 0.7526 (mm) cc_final: 0.6941 (tt)
REVERT: D  586 GLU cc_start: 0.7154 (tt0) cc_final: 0.6912 (tt0)
REVERT: D  615 LEU cc_start: 0.8287 (tt) cc_final: 0.7965 (mt)
  outliers start: 45
  outliers final: 27
  residues processed: 195
  average time/residue: 0.1716
  time to fit residues: 49.0121
Evaluate side-chains
  176 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  205 TYR
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  534 VAL
Chi-restraints excluded: chain D residue  579 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0870
   chunk 31 optimal weight:    0.0980
   chunk 66 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 198 ASN
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 198 ASN
D 228 HIS
D 603 GLN
D 610 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.176878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.144356 restraints weight = 12307.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 2.52
r_work: 0.3638 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9309  Z= 0.131
  Angle     :  0.551   7.512  12696  Z= 0.282
  Chirality :  0.038   0.159   1414
  Planarity :  0.004   0.036   1544
  Dihedral  :  5.166  48.608   1230
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.04 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.25), residues: 1120
  helix:  1.03 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop : -0.66 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 517 
 HIS   0.004   0.001   HIS A 178 
 PHE   0.015   0.001   PHE D  65 
 TYR   0.023   0.001   TYR D 151 
 ARG   0.002   0.000   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04973 (  572)
  hydrogen bonds       : angle       4.99010 ( 1680)
  covalent geometry    : bond        0.00277 ( 9306)
  covalent geometry    : angle       0.55104 (12696)
  Misc. bond           : bond        0.00373 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7557 (mp0)
REVERT: A  133 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8587 (m-80)
REVERT: A  303 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7680 (mmtt)
REVERT: A  342 ASP cc_start: 0.8236 (t0) cc_final: 0.7904 (t0)
REVERT: A  367 TYR cc_start: 0.8015 (t80) cc_final: 0.7605 (t80)
REVERT: A  377 GLU cc_start: 0.7890 (mt-10) cc_final: 0.6981 (mm-30)
REVERT: A  444 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8215 (tt)
REVERT: A  473 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.5453 (t0)
REVERT: A  615 LEU cc_start: 0.8081 (tt) cc_final: 0.7796 (mt)
REVERT: D  122 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7560 (mp0)
REVERT: D  133 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8561 (m-80)
REVERT: D  303 LYS cc_start: 0.8303 (mtmt) cc_final: 0.7664 (mmtt)
REVERT: D  342 ASP cc_start: 0.8167 (t0) cc_final: 0.7836 (t0)
REVERT: D  377 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7135 (mm-30)
REVERT: D  540 PHE cc_start: 0.8880 (t80) cc_final: 0.8640 (t80)
REVERT: D  584 LEU cc_start: 0.7481 (mm) cc_final: 0.6894 (tt)
REVERT: D  615 LEU cc_start: 0.8088 (tt) cc_final: 0.7811 (mt)
  outliers start: 32
  outliers final: 23
  residues processed: 176
  average time/residue: 0.1888
  time to fit residues: 48.2500
Evaluate side-chains
  171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  205 TYR
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  498 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 610 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.168685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.134624 restraints weight = 12486.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.50
r_work: 0.3519 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   9309  Z= 0.199
  Angle     :  0.626   9.285  12696  Z= 0.325
  Chirality :  0.042   0.171   1414
  Planarity :  0.004   0.034   1544
  Dihedral  :  5.316  50.450   1230
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.51 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.25), residues: 1120
  helix:  0.89 (0.19), residues: 758
  sheet:  None (None), residues: 0
  loop : -0.56 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 517 
 HIS   0.007   0.001   HIS D 178 
 PHE   0.020   0.002   PHE A 409 
 TYR   0.018   0.002   TYR D  84 
 ARG   0.002   0.000   ARG A 587 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05887 (  572)
  hydrogen bonds       : angle       5.29959 ( 1680)
  covalent geometry    : bond        0.00466 ( 9306)
  covalent geometry    : angle       0.62573 (12696)
  Misc. bond           : bond        0.00585 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7554 (mp0)
REVERT: A  133 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8699 (m-80)
REVERT: A  367 TYR cc_start: 0.8153 (t80) cc_final: 0.7723 (t80)
REVERT: A  377 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7070 (mm-30)
REVERT: A  473 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.6684 (t0)
REVERT: A  615 LEU cc_start: 0.8155 (tt) cc_final: 0.7839 (mt)
REVERT: D  122 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7553 (mp0)
REVERT: D  133 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8688 (m-80)
REVERT: D  184 ASN cc_start: 0.7017 (m-40) cc_final: 0.6737 (m110)
REVERT: D  189 LYS cc_start: 0.7327 (ttpt) cc_final: 0.6482 (tptt)
REVERT: D  377 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7169 (mm-30)
REVERT: D  584 LEU cc_start: 0.7488 (mm) cc_final: 0.6905 (tt)
REVERT: D  615 LEU cc_start: 0.8196 (tt) cc_final: 0.7892 (mt)
  outliers start: 34
  outliers final: 24
  residues processed: 166
  average time/residue: 0.1802
  time to fit residues: 43.8180
Evaluate side-chains
  152 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  205 TYR
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  579 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 106 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0370
   chunk 68 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7460

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 153 ASN
** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 610 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.172188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.138870 restraints weight = 12480.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.50
r_work: 0.3571 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9309  Z= 0.149
  Angle     :  0.583   7.971  12696  Z= 0.300
  Chirality :  0.039   0.161   1414
  Planarity :  0.004   0.034   1544
  Dihedral  :  5.279  49.793   1230
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 17.83 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.25), residues: 1120
  helix:  0.99 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop : -0.53 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 235 
 HIS   0.004   0.001   HIS D 178 
 PHE   0.016   0.001   PHE D  65 
 TYR   0.021   0.001   TYR D 151 
 ARG   0.005   0.000   ARG D 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05314 (  572)
  hydrogen bonds       : angle       5.18977 ( 1680)
  covalent geometry    : bond        0.00332 ( 9306)
  covalent geometry    : angle       0.58328 (12696)
  Misc. bond           : bond        0.00429 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7527 (mp0)
REVERT: A  133 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8677 (m-80)
REVERT: A  184 ASN cc_start: 0.6840 (m110) cc_final: 0.6510 (m110)
REVERT: A  303 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7704 (mmtt)
REVERT: A  342 ASP cc_start: 0.8236 (t0) cc_final: 0.7857 (t0)
REVERT: A  367 TYR cc_start: 0.8115 (t80) cc_final: 0.7706 (t80)
REVERT: A  377 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7039 (mm-30)
REVERT: A  473 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6354 (t0)
REVERT: A  615 LEU cc_start: 0.8142 (tt) cc_final: 0.7834 (mt)
REVERT: D  133 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8668 (m-80)
REVERT: D  303 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7700 (mmtt)
REVERT: D  342 ASP cc_start: 0.8205 (t0) cc_final: 0.7864 (t0)
REVERT: D  377 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7114 (mm-30)
REVERT: D  584 LEU cc_start: 0.7472 (mm) cc_final: 0.6897 (tt)
REVERT: D  615 LEU cc_start: 0.8160 (tt) cc_final: 0.7860 (mt)
  outliers start: 31
  outliers final: 25
  residues processed: 165
  average time/residue: 0.2091
  time to fit residues: 49.7597
Evaluate side-chains
  162 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  205 TYR
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  579 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.5980
   chunk 57 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 72 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.171620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.138676 restraints weight = 12340.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 2.45
r_work: 0.3572 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.5193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9309  Z= 0.153
  Angle     :  0.585   8.178  12696  Z= 0.303
  Chirality :  0.040   0.187   1414
  Planarity :  0.004   0.034   1544
  Dihedral  :  5.264  50.816   1230
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.51 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.25), residues: 1120
  helix:  1.02 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop : -0.53 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.042   0.002   PHE A 213 
 TYR   0.029   0.001   TYR D 151 
 ARG   0.003   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05299 (  572)
  hydrogen bonds       : angle       5.19598 ( 1680)
  covalent geometry    : bond        0.00342 ( 9306)
  covalent geometry    : angle       0.58455 (12696)
  Misc. bond           : bond        0.00445 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 135
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7537 (mp0)
REVERT: A  133 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8675 (m-80)
REVERT: A  155 ILE cc_start: 0.7870 (mt) cc_final: 0.7328 (tt)
REVERT: A  184 ASN cc_start: 0.6820 (m110) cc_final: 0.6491 (m110)
REVERT: A  303 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7722 (mmtt)
REVERT: A  342 ASP cc_start: 0.8232 (t0) cc_final: 0.7853 (t0)
REVERT: A  367 TYR cc_start: 0.8188 (t80) cc_final: 0.7777 (t80)
REVERT: A  377 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7102 (mm-30)
REVERT: A  473 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6350 (t0)
REVERT: A  615 LEU cc_start: 0.8137 (tt) cc_final: 0.7833 (mt)
REVERT: D  113 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8200 (mt-10)
REVERT: D  133 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8690 (m-80)
REVERT: D  184 ASN cc_start: 0.6862 (m110) cc_final: 0.6587 (m110)
REVERT: D  342 ASP cc_start: 0.8218 (t0) cc_final: 0.7851 (t0)
REVERT: D  377 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7218 (mm-30)
REVERT: D  584 LEU cc_start: 0.7475 (mm) cc_final: 0.6899 (tt)
REVERT: D  615 LEU cc_start: 0.8154 (tt) cc_final: 0.7856 (mt)
  outliers start: 35
  outliers final: 28
  residues processed: 161
  average time/residue: 0.1860
  time to fit residues: 43.8484
Evaluate side-chains
  165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  205 TYR
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  535 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 20 optimal weight:   30.0000
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 ASN
** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 555 ASN
** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.170902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.137811 restraints weight = 12422.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.48
r_work: 0.3563 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.5299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9309  Z= 0.155
  Angle     :  0.591   8.288  12696  Z= 0.306
  Chirality :  0.040   0.194   1414
  Planarity :  0.004   0.034   1544
  Dihedral  :  5.277  51.630   1230
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.62 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.25), residues: 1120
  helix:  1.02 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop : -0.53 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 235 
 HIS   0.004   0.001   HIS D 178 
 PHE   0.039   0.002   PHE D 213 
 TYR   0.029   0.001   TYR D 151 
 ARG   0.002   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05329 (  572)
  hydrogen bonds       : angle       5.19598 ( 1680)
  covalent geometry    : bond        0.00348 ( 9306)
  covalent geometry    : angle       0.59093 (12696)
  Misc. bond           : bond        0.00455 (    3)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 1.102 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7532 (mp0)
REVERT: A  133 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8693 (m-80)
REVERT: A  184 ASN cc_start: 0.6986 (m110) cc_final: 0.6767 (m110)
REVERT: A  342 ASP cc_start: 0.8219 (t0) cc_final: 0.7851 (t0)
REVERT: A  367 TYR cc_start: 0.8187 (t80) cc_final: 0.7802 (t80)
REVERT: A  377 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7131 (mm-30)
REVERT: A  473 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6391 (t0)
REVERT: A  615 LEU cc_start: 0.8169 (tt) cc_final: 0.7878 (mt)
REVERT: D  113 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8207 (mt-10)
REVERT: D  133 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8694 (m-80)
REVERT: D  184 ASN cc_start: 0.6897 (m110) cc_final: 0.6693 (m110)
REVERT: D  189 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6400 (tptt)
REVERT: D  342 ASP cc_start: 0.8187 (t0) cc_final: 0.7838 (t0)
REVERT: D  377 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7254 (mm-30)
REVERT: D  584 LEU cc_start: 0.7464 (mm) cc_final: 0.6880 (tt)
REVERT: D  615 LEU cc_start: 0.8190 (tt) cc_final: 0.7898 (mt)
  outliers start: 35
  outliers final: 30
  residues processed: 157
  average time/residue: 0.1700
  time to fit residues: 39.9635
Evaluate side-chains
  161 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  205 TYR
Chi-restraints excluded: chain A residue  228 HIS
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  579 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 75 optimal weight:    0.0020
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.9190

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.171137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.137923 restraints weight = 12349.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.46
r_work: 0.3557 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.5345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9309  Z= 0.159
  Angle     :  0.594   9.577  12696  Z= 0.308
  Chirality :  0.040   0.198   1414
  Planarity :  0.004   0.034   1544
  Dihedral  :  5.293  51.865   1230
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.93 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.25), residues: 1120
  helix:  0.99 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -0.64 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 178 
 PHE   0.037   0.002   PHE D 213 
 TYR   0.029   0.001   TYR D 151 
 ARG   0.002   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05357 (  572)
  hydrogen bonds       : angle       5.21371 ( 1680)
  covalent geometry    : bond        0.00359 ( 9306)
  covalent geometry    : angle       0.59448 (12696)
  Misc. bond           : bond        0.00463 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4197.68 seconds
wall clock time: 73 minutes 34.48 seconds (4414.48 seconds total)