Starting phenix.real_space_refine
on Tue Mar 11 15:09:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nqk_12528/03_2025/7nqk_12528.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nqk_12528/03_2025/7nqk_12528.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nqk_12528/03_2025/7nqk_12528.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nqk_12528/03_2025/7nqk_12528.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nqk_12528/03_2025/7nqk_12528.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nqk_12528/03_2025/7nqk_12528.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.044
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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    3998      2.51       5
     N    1014      2.21       5
     O    1090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6139
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 658, 5173
          Classifications: {'peptide': 658}
          Link IDs: {'PTRANS': 24, 'TRANS': 633}
    Chain: "B"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 966
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
  Time building chain proxies: 4.44, per 1000 atoms: 0.72
  Number of scatterers: 6139
  At special positions: 0
  Unit cell: (103.168, 113.984, 93.184, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1090      8.00
     N    1014      7.00
     C    3998      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS A 216 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 936.6 milliseconds
  

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1456

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      46.1% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 46 through 74
      removed outlier: 3.625A  pdb=" N   VAL A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   ASN A  52 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A  59 " --> pdb=" O   CYS A  55 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A  66 " --> pdb=" O   GLY A  62 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A  67 " --> pdb=" O   MET A  63 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   THR A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   LEU A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 96
    Processing helix  chain 'A' and resid 96 through 106
      removed outlier: 4.042A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 130
      removed outlier: 3.572A  pdb=" N   TYR A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   VAL A 120 " --> pdb=" O   TYR A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 171
      removed outlier: 3.533A  pdb=" N   SER A 146 " --> pdb=" O   HIS A 142 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   GLY A 159 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      Proline residue:  A 162  - end of helix
      removed outlier: 3.757A  pdb=" N   ALA A 165 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 202
      removed outlier: 4.032A  pdb=" N   ARG A 182 " --> pdb=" O   GLU A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 205
      No H-bonds generated for 'chain 'A' and resid 203 through 205'
    Processing helix  chain 'A' and resid 217 through 237
      Proline residue:  A 224  - end of helix
      removed outlier: 3.548A  pdb=" N   VAL A 233 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 241
    Processing helix  chain 'A' and resid 250 through 263
    Processing helix  chain 'A' and resid 289 through 306
      removed outlier: 3.635A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ASP A 295 " --> pdb=" O   HIS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 318
      removed outlier: 3.763A  pdb=" N   PHE A 312 " --> pdb=" O   PRO A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 328
    Processing helix  chain 'A' and resid 340 through 345
    Processing helix  chain 'A' and resid 346 through 362
      removed outlier: 3.608A  pdb=" N   PHE A 350 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      Proline residue:  A 357  - end of helix
    Processing helix  chain 'A' and resid 362 through 368
    Processing helix  chain 'A' and resid 377 through 402
    Processing helix  chain 'A' and resid 611 through 636
      removed outlier: 3.612A  pdb=" N   VAL A 627 " --> pdb=" O   VAL A 623 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   THR A 628 " --> pdb=" O   MET A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 642
      removed outlier: 4.132A  pdb=" N   LYS A 642 " --> pdb=" O   SER A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 665
      removed outlier: 4.141A  pdb=" N   GLN A 665 " --> pdb=" O   LEU A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 695
      removed outlier: 3.685A  pdb=" N   TYR A 695 " --> pdb=" O   VAL A 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 30
      No H-bonds generated for 'chain 'B' and resid 28 through 30'
    Processing helix  chain 'B' and resid 53 through 56
      removed outlier: 3.801A  pdb=" N   ARG B  56 " --> pdb=" O   TRP B  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 53 through 56'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 455
      removed outlier: 3.538A  pdb=" N   LEU A 416 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A 414 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   PHE A 415 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   LEU A 489 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   GLN A 417 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   ILE A 491 " --> pdb=" O   GLN A 417 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   LEU A 419 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
      removed outlier: 8.814A  pdb=" N   GLN A 493 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   CYS A 486 " --> pdb=" O   ASP A 505 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 443
    Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443
      removed outlier: 3.832A  pdb=" N   LEU A 464 " --> pdb=" O   HIS A 479 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS A 479 " --> pdb=" O   LEU A 464 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545
      removed outlier: 3.588A  pdb=" N   ASN A 521 " --> pdb=" O   GLY A 544 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545
      removed outlier: 3.588A  pdb=" N   ASN A 521 " --> pdb=" O   GLY A 544 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 556
    Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 562
    Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 23
    Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 60
      removed outlier: 5.360A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)

    317 hydrogen bonds defined for protein.
    891 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: 1.92

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1908
        1.34 -     1.46: 1510
        1.46 -     1.58: 2816
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6292
  Sorted by residual:
  bond pdb=" N   GLY B  10 "
       pdb=" CA  GLY B  10 "
    ideal  model  delta    sigma   weight residual
    1.443  1.485 -0.043 1.17e-02 7.31e+03 1.32e+01
  bond pdb=" CA  SER B   7 "
       pdb=" CB  SER B   7 "
    ideal  model  delta    sigma   weight residual
    1.535  1.485  0.049 1.58e-02 4.01e+03 9.80e+00
  bond pdb=" N   LEU B  11 "
       pdb=" CA  LEU B  11 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.039 1.32e-02 5.74e+03 8.91e+00
  bond pdb=" N   GLY B   9 "
       pdb=" CA  GLY B   9 "
    ideal  model  delta    sigma   weight residual
    1.449  1.486 -0.037 1.24e-02 6.50e+03 8.77e+00
  bond pdb=" N   GLU B   6 "
       pdb=" CA  GLU B   6 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.29e-02 6.01e+03 8.62e+00
  ... (remaining 6287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 8328
        2.25 -     4.51: 183
        4.51 -     6.76: 27
        6.76 -     9.01: 4
        9.01 -    11.26: 3
  Bond angle restraints: 8545
  Sorted by residual:
  angle pdb=" CA  GLY B   9 "
        pdb=" C   GLY B   9 "
        pdb=" N   GLY B  10 "
      ideal   model   delta    sigma   weight residual
     114.48  120.99   -6.51 1.19e+00 7.06e-01 3.00e+01
  angle pdb=" CA  GLY B   9 "
        pdb=" C   GLY B   9 "
        pdb=" O   GLY B   9 "
      ideal   model   delta    sigma   weight residual
     121.87  116.39    5.48 1.02e+00 9.61e-01 2.88e+01
  angle pdb=" CA  THR B 124 "
        pdb=" C   THR B 124 "
        pdb=" O   THR B 124 "
      ideal   model   delta    sigma   weight residual
     121.60  115.98    5.62 1.21e+00 6.83e-01 2.15e+01
  angle pdb=" CA  CYS A 211 "
        pdb=" CB  CYS A 211 "
        pdb=" SG  CYS A 211 "
      ideal   model   delta    sigma   weight residual
     114.40  124.86  -10.46 2.30e+00 1.89e-01 2.07e+01
  angle pdb=" CA  VAL B   5 "
        pdb=" C   VAL B   5 "
        pdb=" O   VAL B   5 "
      ideal   model   delta    sigma   weight residual
     122.13  117.66    4.47 1.11e+00 8.12e-01 1.62e+01
  ... (remaining 8540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 3275
       17.45 -    34.90: 338
       34.90 -    52.35: 58
       52.35 -    69.80: 13
       69.80 -    87.24: 9
  Dihedral angle restraints: 3693
    sinusoidal: 1426
      harmonic: 2267
  Sorted by residual:
  dihedral pdb=" CA  LYS A 210 "
           pdb=" C   LYS A 210 "
           pdb=" N   CYS A 211 "
           pdb=" CA  CYS A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.31  -37.69     0      5.00e+00 4.00e-02 5.68e+01
  dihedral pdb=" CA  VAL A 209 "
           pdb=" C   VAL A 209 "
           pdb=" N   LYS A 210 "
           pdb=" CA  LYS A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.85  -26.15     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  TRP A 283 "
           pdb=" C   TRP A 283 "
           pdb=" N   ALA A 284 "
           pdb=" CA  ALA A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.02   24.98     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 3690 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 819
       0.063 -    0.126: 132
       0.126 -    0.188: 17
       0.188 -    0.251: 2
       0.251 -    0.314: 1
  Chirality restraints: 971
  Sorted by residual:
  chirality pdb=" CB  VAL B   5 "
            pdb=" CA  VAL B   5 "
            pdb=" CG1 VAL B   5 "
            pdb=" CG2 VAL B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CB  VAL B 123 "
            pdb=" CA  VAL B 123 "
            pdb=" CG1 VAL B 123 "
            pdb=" CG2 VAL B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  ASP B  90 "
            pdb=" N   ASP B  90 "
            pdb=" C   ASP B  90 "
            pdb=" CB  ASP B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.94e-01
  ... (remaining 968 not shown)

  Planarity restraints: 1067
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 280 "   -0.020 2.00e-02 2.50e+03   2.18e-02 1.19e+01
        pdb=" CG  TRP A 280 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 280 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 280 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 280 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 280 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 280 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 280 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 280 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 280 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 210 "   -0.012 2.00e-02 2.50e+03   2.44e-02 5.93e+00
        pdb=" C   LYS A 210 "    0.042 2.00e-02 2.50e+03
        pdb=" O   LYS A 210 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   CYS A 211 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  89 "   -0.011 2.00e-02 2.50e+03   2.18e-02 4.75e+00
        pdb=" C   ARG B  89 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ARG B  89 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP B  90 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1064 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 76
        2.61 -     3.18: 5686
        3.18 -     3.75: 9220
        3.75 -     4.33: 12704
        4.33 -     4.90: 20703
  Nonbonded interactions: 48389
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 423 "
            pdb=" OH  TYR A 470 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" NH1 ARG A 322 "
            pdb=" OE2 GLU A 674 "
     model   vdw
     2.122 3.120
  nonbonded pdb=" OG1 THR A 533 "
            pdb=" OD2 ASP B  73 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   SER A 321 "
            pdb=" OG1 THR A 324 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OH  TYR A 306 "
            pdb=" OG  SER A 633 "
     model   vdw
     2.207 3.040
  ... (remaining 48384 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.930
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
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      :  0.005   0.049   6292  Z= 0.324
  Angle     :  0.841  11.263   8545  Z= 0.481
  Chirality :  0.049   0.314    971
  Planarity :  0.004   0.043   1067
  Dihedral  : 14.925  87.244   2231
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  0.75 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.81 (0.31), residues: 777
  helix:  0.17 (0.29), residues: 332
  sheet: -1.51 (0.40), residues: 166
  loop : -2.63 (0.39), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 280 
 HIS   0.006   0.001   HIS A 476 
 PHE   0.019   0.002   PHE A 355 
 TYR   0.022   0.002   TYR A 121 
 ARG   0.011   0.001   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 159
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8070 (tp30) cc_final: 0.7626 (tp30)
REVERT: A  105 ASP cc_start: 0.8431 (m-30) cc_final: 0.8104 (m-30)
REVERT: A  147 LEU cc_start: 0.9140 (mm) cc_final: 0.8927 (mm)
REVERT: A  228 MET cc_start: 0.8136 (tmm) cc_final: 0.7803 (tmm)
REVERT: B   11 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7358 (tt)
  outliers start: 6
  outliers final: 2
  residues processed: 165
  average time/residue: 0.1636
  time to fit residues: 36.5207
Evaluate side-chains
  127 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 124
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0770
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 318 GLN
A 345 GLN
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 521 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.106265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.094173 restraints weight = 14537.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.096689 restraints weight = 6242.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.098221 restraints weight = 3515.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6292  Z= 0.203
  Angle     :  0.680   8.735   8545  Z= 0.354
  Chirality :  0.044   0.185    971
  Planarity :  0.005   0.050   1067
  Dihedral  :  6.344  53.086    844
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.63 %
    Favored  : 84.96 %
  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: -1.42 (0.31), residues: 777
  helix:  0.61 (0.29), residues: 338
  sheet: -1.57 (0.39), residues: 174
  loop : -2.47 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 280 
 HIS   0.002   0.001   HIS A 406 
 PHE   0.012   0.001   PHE A 111 
 TYR   0.013   0.001   TYR A 121 
 ARG   0.004   0.001   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8303 (tp30) cc_final: 0.7788 (tp30)
REVERT: A  105 ASP cc_start: 0.8630 (m-30) cc_final: 0.8204 (m-30)
REVERT: A  147 LEU cc_start: 0.9157 (mm) cc_final: 0.8892 (mm)
REVERT: A  228 MET cc_start: 0.8210 (tmm) cc_final: 0.7918 (tmm)
REVERT: A  622 GLU cc_start: 0.7980 (tp30) cc_final: 0.7774 (tp30)
REVERT: B  109 ASN cc_start: 0.9079 (p0) cc_final: 0.8799 (p0)
  outliers start: 16
  outliers final: 14
  residues processed: 163
  average time/residue: 0.1557
  time to fit residues: 34.6305
Evaluate side-chains
  152 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 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 = 0.3543 r_free = 0.3543 target = 0.105718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.093579 restraints weight = 14597.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.096044 restraints weight = 6359.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.097608 restraints weight = 3609.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6292  Z= 0.204
  Angle     :  0.640   9.083   8545  Z= 0.332
  Chirality :  0.043   0.164    971
  Planarity :  0.005   0.053   1067
  Dihedral  :  5.674  44.615    842
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.59 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.32), residues: 777
  helix:  0.92 (0.29), residues: 333
  sheet: -1.60 (0.38), residues: 180
  loop : -2.26 (0.42), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 280 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.009   0.001   PHE A 111 
 TYR   0.010   0.001   TYR A 121 
 ARG   0.005   0.001   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A  105 ASP cc_start: 0.8668 (m-30) cc_final: 0.8238 (m-30)
REVERT: A  147 LEU cc_start: 0.9157 (mm) cc_final: 0.8889 (mm)
REVERT: A  228 MET cc_start: 0.8212 (tmm) cc_final: 0.8011 (tmm)
REVERT: A  622 GLU cc_start: 0.8013 (tp30) cc_final: 0.7701 (tp30)
REVERT: B   43 LYS cc_start: 0.8259 (tmtt) cc_final: 0.8030 (tmtt)
REVERT: B  109 ASN cc_start: 0.9057 (p0) cc_final: 0.8759 (p0)
  outliers start: 21
  outliers final: 19
  residues processed: 158
  average time/residue: 0.1631
  time to fit residues: 35.2190
Evaluate side-chains
  153 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 70 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 66 optimal weight:    0.2980
   chunk 1 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 171 GLN
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 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 = 0.3496 r_free = 0.3496 target = 0.102449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090654 restraints weight = 15063.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.093897 restraints weight = 6714.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.095409 restraints weight = 3223.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6292  Z= 0.317
  Angle     :  0.685   8.973   8545  Z= 0.358
  Chirality :  0.045   0.168    971
  Planarity :  0.005   0.053   1067
  Dihedral  :  5.757  42.737    842
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 19.25 %
    Favored  : 76.24 %
  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: -1.10 (0.32), residues: 777
  helix:  0.90 (0.29), residues: 336
  sheet: -1.52 (0.39), residues: 178
  loop : -2.25 (0.42), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.011   0.001   PHE A 111 
 TYR   0.012   0.001   TYR B 114 
 ARG   0.006   0.001   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8482 (tp30) cc_final: 0.7682 (tp30)
REVERT: A   96 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8848 (p)
REVERT: A  147 LEU cc_start: 0.9199 (mm) cc_final: 0.8900 (mm)
REVERT: A  204 MET cc_start: 0.7931 (tpt) cc_final: 0.6873 (tmm)
REVERT: A  350 PHE cc_start: 0.8474 (t80) cc_final: 0.8238 (t80)
REVERT: A  389 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8924 (mp)
REVERT: A  406 HIS cc_start: 0.5624 (OUTLIER) cc_final: 0.4743 (p90)
REVERT: A  514 MET cc_start: 0.7514 (ttm) cc_final: 0.7255 (ttt)
  outliers start: 30
  outliers final: 25
  residues processed: 154
  average time/residue: 0.1570
  time to fit residues: 33.1123
Evaluate side-chains
  157 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 65 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 26 optimal weight:    0.2980
   chunk 11 optimal weight:    0.8980
   chunk 66 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.104570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.092806 restraints weight = 14780.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.096119 restraints weight = 6641.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.097610 restraints weight = 3173.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6292  Z= 0.215
  Angle     :  0.644  11.306   8545  Z= 0.332
  Chirality :  0.043   0.164    971
  Planarity :  0.005   0.052   1067
  Dihedral  :  5.527  36.259    842
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 20.30 %
    Favored  : 75.34 %
  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: -0.95 (0.32), residues: 777
  helix:  1.06 (0.29), residues: 327
  sheet: -1.47 (0.39), residues: 178
  loop : -2.09 (0.42), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.012   0.001   PHE A 111 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.005   0.000   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8434 (tp30) cc_final: 0.7717 (tp30)
REVERT: A   96 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8817 (p)
REVERT: A  105 ASP cc_start: 0.8715 (m-30) cc_final: 0.8255 (m-30)
REVERT: A  147 LEU cc_start: 0.9166 (mm) cc_final: 0.8891 (mm)
REVERT: A  204 MET cc_start: 0.7847 (tpt) cc_final: 0.6806 (tmm)
REVERT: A  228 MET cc_start: 0.8119 (tmm) cc_final: 0.7680 (tmm)
REVERT: A  350 PHE cc_start: 0.8368 (t80) cc_final: 0.8119 (t80)
REVERT: A  406 HIS cc_start: 0.5512 (OUTLIER) cc_final: 0.4822 (p90)
REVERT: A  534 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7438 (p0)
  outliers start: 29
  outliers final: 20
  residues processed: 155
  average time/residue: 0.1479
  time to fit residues: 31.5392
Evaluate side-chains
  153 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0270
   chunk 21 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.1844

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 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 = 0.3527 r_free = 0.3527 target = 0.104474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.092785 restraints weight = 14653.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.096043 restraints weight = 6589.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.097599 restraints weight = 3164.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6292  Z= 0.226
  Angle     :  0.639  11.085   8545  Z= 0.328
  Chirality :  0.043   0.154    971
  Planarity :  0.005   0.052   1067
  Dihedral  :  5.391  29.348    842
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 20.45 %
    Favored  : 75.04 %
  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: -0.95 (0.32), residues: 777
  helix:  1.07 (0.29), residues: 327
  sheet: -1.47 (0.39), residues: 179
  loop : -2.10 (0.41), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.011   0.001   PHE A 111 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.006   0.001   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8481 (tp30) cc_final: 0.7659 (tp30)
REVERT: A   96 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8838 (p)
REVERT: A  147 LEU cc_start: 0.9148 (mm) cc_final: 0.8868 (mm)
REVERT: A  204 MET cc_start: 0.7836 (tpt) cc_final: 0.6818 (tmm)
REVERT: A  212 PHE cc_start: 0.6528 (m-80) cc_final: 0.6281 (m-80)
REVERT: A  228 MET cc_start: 0.8183 (tmm) cc_final: 0.7949 (tmm)
REVERT: A  350 PHE cc_start: 0.8345 (t80) cc_final: 0.8104 (t80)
REVERT: A  406 HIS cc_start: 0.5380 (OUTLIER) cc_final: 0.4696 (p90)
REVERT: A  534 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7447 (p0)
REVERT: A  622 GLU cc_start: 0.7993 (tp30) cc_final: 0.7705 (tp30)
  outliers start: 30
  outliers final: 21
  residues processed: 159
  average time/residue: 0.1595
  time to fit residues: 34.9921
Evaluate side-chains
  159 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0570
   chunk 56 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 65 optimal weight:    9.9990
   chunk 58 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 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 = 0.3572 r_free = 0.3572 target = 0.107411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.095717 restraints weight = 14717.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.098851 restraints weight = 6513.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.100461 restraints weight = 3210.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6292  Z= 0.170
  Angle     :  0.633   9.500   8545  Z= 0.320
  Chirality :  0.042   0.162    971
  Planarity :  0.004   0.052   1067
  Dihedral  :  5.141  20.998    842
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.11 %
    Favored  : 74.29 %
  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: -0.85 (0.32), residues: 777
  helix:  1.16 (0.29), residues: 327
  sheet: -1.35 (0.40), residues: 177
  loop : -2.12 (0.41), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 280 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.009   0.001   PHE A 111 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.006   0.000   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8397 (tp30) cc_final: 0.7686 (tp30)
REVERT: A  147 LEU cc_start: 0.9070 (mm) cc_final: 0.8836 (mm)
REVERT: A  212 PHE cc_start: 0.6529 (m-80) cc_final: 0.6302 (m-80)
REVERT: A  228 MET cc_start: 0.8149 (tmm) cc_final: 0.7918 (tmm)
REVERT: A  350 PHE cc_start: 0.8254 (t80) cc_final: 0.8046 (t80)
REVERT: A  406 HIS cc_start: 0.5351 (OUTLIER) cc_final: 0.4751 (p90)
REVERT: A  534 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7438 (p0)
REVERT: A  553 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8465 (ptm-80)
REVERT: A  622 GLU cc_start: 0.7948 (tp30) cc_final: 0.7655 (tp30)
REVERT: B   76 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8334 (pttm)
REVERT: B  109 ASN cc_start: 0.9003 (p0) cc_final: 0.8712 (p0)
  outliers start: 24
  outliers final: 15
  residues processed: 165
  average time/residue: 0.1734
  time to fit residues: 38.0903
Evaluate side-chains
  158 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 43 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 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 = 0.3563 r_free = 0.3563 target = 0.106840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.095152 restraints weight = 14501.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.098411 restraints weight = 6480.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.099931 restraints weight = 3106.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6292  Z= 0.195
  Angle     :  0.657  12.397   8545  Z= 0.330
  Chirality :  0.043   0.183    971
  Planarity :  0.005   0.077   1067
  Dihedral  :  5.114  20.731    841
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 22.26 %
    Favored  : 74.29 %
  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: -0.85 (0.32), residues: 777
  helix:  1.16 (0.29), residues: 327
  sheet: -1.36 (0.40), residues: 178
  loop : -2.10 (0.41), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 280 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.010   0.001   PHE A  58 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.007   0.000   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8430 (tp30) cc_final: 0.7840 (tp30)
REVERT: A   57 ARG cc_start: 0.8768 (mmm160) cc_final: 0.8522 (tpp-160)
REVERT: A  130 LEU cc_start: 0.9124 (tp) cc_final: 0.8924 (tp)
REVERT: A  147 LEU cc_start: 0.9073 (mm) cc_final: 0.8829 (mm)
REVERT: A  204 MET cc_start: 0.7777 (tpt) cc_final: 0.6715 (tmm)
REVERT: A  212 PHE cc_start: 0.6584 (m-80) cc_final: 0.6361 (m-80)
REVERT: A  228 MET cc_start: 0.8161 (tmm) cc_final: 0.7916 (tmm)
REVERT: A  406 HIS cc_start: 0.5202 (OUTLIER) cc_final: 0.4612 (p90)
REVERT: A  534 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7483 (p0)
REVERT: A  553 ARG cc_start: 0.8697 (ptm-80) cc_final: 0.8447 (ptm-80)
REVERT: B  109 ASN cc_start: 0.9012 (p0) cc_final: 0.8786 (p0)
  outliers start: 23
  outliers final: 17
  residues processed: 158
  average time/residue: 0.1637
  time to fit residues: 34.8594
Evaluate side-chains
  158 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 20 optimal weight:    0.4980
   chunk 49 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 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 = 0.3552 r_free = 0.3552 target = 0.106088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.094304 restraints weight = 14817.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.097625 restraints weight = 6673.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.099236 restraints weight = 3171.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6292  Z= 0.220
  Angle     :  0.678  11.338   8545  Z= 0.344
  Chirality :  0.044   0.195    971
  Planarity :  0.005   0.052   1067
  Dihedral  :  5.170  21.249    841
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.86 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.32), residues: 777
  helix:  1.20 (0.29), residues: 327
  sheet: -1.36 (0.40), residues: 178
  loop : -2.09 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.032   0.001   PHE A  58 
 TYR   0.009   0.001   TYR A 183 
 ARG   0.008   0.001   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8452 (tp30) cc_final: 0.7626 (tp30)
REVERT: A  147 LEU cc_start: 0.9091 (mm) cc_final: 0.8838 (mm)
REVERT: A  204 MET cc_start: 0.7787 (tpt) cc_final: 0.6805 (tmm)
REVERT: A  212 PHE cc_start: 0.6570 (m-80) cc_final: 0.6327 (m-80)
REVERT: A  228 MET cc_start: 0.8217 (tmm) cc_final: 0.7945 (tmm)
REVERT: A  350 PHE cc_start: 0.8368 (t80) cc_final: 0.8078 (t80)
REVERT: A  406 HIS cc_start: 0.5144 (OUTLIER) cc_final: 0.4558 (p90)
  outliers start: 22
  outliers final: 17
  residues processed: 152
  average time/residue: 0.1512
  time to fit residues: 31.5964
Evaluate side-chains
  154 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 109 ASN ** 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 = 0.3546 r_free = 0.3546 target = 0.105809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.093988 restraints weight = 14732.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.097263 restraints weight = 6678.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.098764 restraints weight = 3221.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6292  Z= 0.224
  Angle     :  0.685  12.992   8545  Z= 0.345
  Chirality :  0.044   0.196    971
  Planarity :  0.004   0.041   1067
  Dihedral  :  5.154  21.587    841
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 23.76 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.32), residues: 777
  helix:  1.23 (0.29), residues: 327
  sheet: -1.34 (0.40), residues: 178
  loop : -2.05 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.026   0.001   PHE A  58 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.009   0.001   ARG B  56 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8470 (tp30) cc_final: 0.7685 (tp30)
REVERT: A  147 LEU cc_start: 0.9084 (mm) cc_final: 0.8825 (mm)
REVERT: A  204 MET cc_start: 0.7807 (tpt) cc_final: 0.6829 (tmm)
REVERT: A  212 PHE cc_start: 0.6601 (m-80) cc_final: 0.6356 (m-80)
REVERT: A  350 PHE cc_start: 0.8389 (t80) cc_final: 0.8085 (t80)
REVERT: A  406 HIS cc_start: 0.5164 (OUTLIER) cc_final: 0.4559 (p90)
REVERT: A  450 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8616 (t)
  outliers start: 21
  outliers final: 17
  residues processed: 150
  average time/residue: 0.1529
  time to fit residues: 31.6019
Evaluate side-chains
  156 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0980
   chunk 46 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0570
   chunk 52 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.107973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.096013 restraints weight = 14903.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.099305 restraints weight = 6638.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.100906 restraints weight = 3229.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6292  Z= 0.180
  Angle     :  0.664  12.284   8545  Z= 0.333
  Chirality :  0.043   0.190    971
  Planarity :  0.004   0.041   1067
  Dihedral  :  5.003  20.274    841
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.46 %
    Favored  : 73.68 %
  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 (0.32), residues: 777
  helix:  1.24 (0.29), residues: 327
  sheet: -1.25 (0.40), residues: 178
  loop : -2.04 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 649 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.028   0.001   PHE A  58 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.008   0.000   ARG B  56 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2272.47 seconds
wall clock time: 40 minutes 5.83 seconds (2405.83 seconds total)