Starting phenix.real_space_refine
on Sun Oct 13 11:13:21 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/10_2024/8ta3_41127.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/10_2024/8ta3_41127.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/10_2024/8ta3_41127.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/10_2024/8ta3_41127.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/10_2024/8ta3_41127.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/10_2024/8ta3_41127.cif"
  }
  resolution = 2.46
  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=   0.198
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      46      5.16       5
     Cl      2      4.86       5
     C    4825      2.51       5
     N    1194      2.21       5
     O    1225      1.98       5
     H    7545      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib"
  Total number of atoms: 14837
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 7406
          Classifications: {'peptide': 470}
          Link IDs: {'PTRANS': 22, 'TRANS': 447}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 7429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 7429
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 22, 'TRANS': 449}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.60, per 1000 atoms: 0.51
  Number of scatterers: 14837
  At special positions: 0
  Unit cell: (78.518, 75.68, 117.304, 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      46     16.00
     O    1225      8.00
     N    1194      7.00
     C    4825      6.00
     H    7545      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.12
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 3 sheets defined
      76.9% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 126
      removed outlier: 3.520A  pdb=" N   ALA A 102 " --> pdb=" O   GLY A  98 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN A 119 " --> pdb=" O   CYS A 115 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLN A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 156
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 157 through 160
      removed outlier: 3.661A  pdb=" N   VAL A 160 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 157 through 160'
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 181 through 198
      removed outlier: 3.558A  pdb=" N   SER A 198 " --> pdb=" O   CYS A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 223
    Processing helix  chain 'A' and resid 234 through 253
      removed outlier: 3.594A  pdb=" N   ALA A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 267
    Processing helix  chain 'A' and resid 272 through 296
      removed outlier: 3.676A  pdb=" N   VAL A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 320 through 352
      removed outlier: 3.506A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 335 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL A 346 " --> pdb=" O   ASN A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 362
      removed outlier: 4.061A  pdb=" N   PHE A 358 " --> pdb=" O   THR A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 379
    Processing helix  chain 'A' and resid 382 through 388
      removed outlier: 3.967A  pdb=" N   GLN A 385 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA A 388 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 401
    Processing helix  chain 'A' and resid 421 through 425
    Processing helix  chain 'A' and resid 430 through 450
      removed outlier: 3.773A  pdb=" N   TRP A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 481
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 3.920A  pdb=" N   TYR A 499 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA A 508 " --> pdb=" O   ALA A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 526
    Processing helix  chain 'A' and resid 530 through 547
      removed outlier: 3.662A  pdb=" N   SER A 547 " --> pdb=" O   ALA A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'B' and resid 89 through 125
    Processing helix  chain 'B' and resid 129 through 156
      removed outlier: 3.611A  pdb=" N   TYR B 140 " --> pdb=" O   ALA B 136 " (cutoff:3.500A)
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 157 through 160
    Processing helix  chain 'B' and resid 163 through 172
      removed outlier: 3.509A  pdb=" N   ARG B 172 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 198
    Processing helix  chain 'B' and resid 204 through 223
    Processing helix  chain 'B' and resid 232 through 253
      removed outlier: 3.714A  pdb=" N   ALA B 242 " --> pdb=" O   GLU B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 267
      removed outlier: 3.511A  pdb=" N   VAL B 259 " --> pdb=" O   PRO B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 293
    Processing helix  chain 'B' and resid 317 through 319
      No H-bonds generated for 'chain 'B' and resid 317 through 319'
    Processing helix  chain 'B' and resid 320 through 352
      removed outlier: 3.581A  pdb=" N   PHE B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B 346 " --> pdb=" O   ASN B 342 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   MET B 349 " --> pdb=" O   ILE B 345 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLN B 352 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 360
    Processing helix  chain 'B' and resid 364 through 379
    Processing helix  chain 'B' and resid 382 through 388
      removed outlier: 4.141A  pdb=" N   GLN B 385 " --> pdb=" O   GLY B 382 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA B 388 " --> pdb=" O   GLN B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 401
    Processing helix  chain 'B' and resid 420 through 425
    Processing helix  chain 'B' and resid 430 through 450
      removed outlier: 3.881A  pdb=" N   TRP B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 481
      removed outlier: 3.548A  pdb=" N   ILE B 465 " --> pdb=" O   PRO B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 3.945A  pdb=" N   TYR B 499 " --> pdb=" O   VAL B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 526
    Processing helix  chain 'B' and resid 530 through 547
      removed outlier: 3.948A  pdb=" N   SER B 547 " --> pdb=" O   ALA B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 560
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18
    Processing sheet with id=AA2, first strand: chain 'A' and resid 269 through 271
      removed outlier: 3.656A  pdb=" N   PHE A 270 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE B 270 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 18

    528 hydrogen bonds defined for protein.
    1542 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: 4.77

  Time building geometry restraints manager: 4.64 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 7531
        1.12 -     1.30: 1106
        1.30 -     1.47: 2809
        1.47 -     1.65: 3489
        1.65 -     1.82: 78
  Bond restraints: 15013
  Sorted by residual:
  bond pdb=" N   LEU A 318 "
       pdb=" H   LEU A 318 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   THR A 169 "
       pdb=" H   THR A 169 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   LEU B 318 "
       pdb=" H   LEU B 318 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" NE  ARG A 471 "
       pdb=" HE  ARG A 471 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   LYS A 221 "
       pdb=" H   LYS A 221 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 15008 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 22741
        2.57 -     5.14: 3474
        5.14 -     7.71: 913
        7.71 -    10.28: 32
       10.28 -    12.85: 14
  Bond angle restraints: 27174
  Sorted by residual:
  angle pdb=" CA  ASP B 402 "
        pdb=" CB  ASP B 402 "
        pdb=" CG  ASP B 402 "
      ideal   model   delta    sigma   weight residual
     112.60  118.97   -6.37 1.00e+00 1.00e+00 4.06e+01
  angle pdb=" N   PRO B 426 "
        pdb=" CA  PRO B 426 "
        pdb=" CB  PRO B 426 "
      ideal   model   delta    sigma   weight residual
     103.19  106.58   -3.39 5.60e-01 3.19e+00 3.65e+01
  angle pdb=" CA  PHE B 401 "
        pdb=" CB  PHE B 401 "
        pdb=" CG  PHE B 401 "
      ideal   model   delta    sigma   weight residual
     113.80  119.64   -5.84 1.00e+00 1.00e+00 3.41e+01
  angle pdb=" CA  PHE A 401 "
        pdb=" CB  PHE A 401 "
        pdb=" CG  PHE A 401 "
      ideal   model   delta    sigma   weight residual
     113.80  119.44   -5.64 1.00e+00 1.00e+00 3.18e+01
  angle pdb=" CD  ARG A 471 "
        pdb=" NE  ARG A 471 "
        pdb=" CZ  ARG A 471 "
      ideal   model   delta    sigma   weight residual
     124.40  132.27   -7.87 1.40e+00 5.10e-01 3.16e+01
  ... (remaining 27169 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.64: 6392
       16.64 -    33.29: 345
       33.29 -    49.93: 101
       49.93 -    66.57: 208
       66.57 -    83.22: 18
  Dihedral angle restraints: 7064
    sinusoidal: 3756
      harmonic: 3308
  Sorted by residual:
  dihedral pdb=" CA  LEU B 176 "
           pdb=" C   LEU B 176 "
           pdb=" N   LYS B 177 "
           pdb=" CA  LYS B 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.02  -28.98     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  LEU A 176 "
           pdb=" C   LEU A 176 "
           pdb=" N   LYS A 177 "
           pdb=" CA  LYS A 177 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.68  -27.32     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  GLU B 231 "
           pdb=" C   GLU B 231 "
           pdb=" N   ASN B 232 "
           pdb=" CA  ASN B 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.62   26.38     0      5.00e+00 4.00e-02 2.78e+01
  ... (remaining 7061 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 788
       0.078 -    0.155: 304
       0.155 -    0.232: 87
       0.232 -    0.310: 15
       0.310 -    0.387: 4
  Chirality restraints: 1198
  Sorted by residual:
  chirality pdb=" CA  PRO A 380 "
            pdb=" N   PRO A 380 "
            pdb=" C   PRO A 380 "
            pdb=" CB  PRO A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.33    0.39 2.00e-01 2.50e+01 3.74e+00
  chirality pdb=" CA  PRO B 380 "
            pdb=" N   PRO B 380 "
            pdb=" C   PRO B 380 "
            pdb=" CB  PRO B 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.35    0.37 2.00e-01 2.50e+01 3.43e+00
  chirality pdb=" CA  THR A 420 "
            pdb=" N   THR A 420 "
            pdb=" C   THR A 420 "
            pdb=" CB  THR A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.16    0.37 2.00e-01 2.50e+01 3.40e+00
  ... (remaining 1195 not shown)

  Planarity restraints: 2129
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 363 "    0.269 9.50e-02 1.11e+02   1.37e-01 2.51e+02
        pdb=" NE  ARG A 363 "    0.097 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 363 "    0.068 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 363 "    0.043 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 363 "    0.045 2.00e-02 2.50e+03
        pdb="HH11 ARG A 363 "   -0.216 2.00e-02 2.50e+03
        pdb="HH12 ARG A 363 "    0.102 2.00e-02 2.50e+03
        pdb="HH21 ARG A 363 "   -0.149 2.00e-02 2.50e+03
        pdb="HH22 ARG A 363 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 106 "    0.144 2.00e-02 2.50e+03   5.38e-02 1.16e+02
        pdb=" CG  TRP A 106 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 106 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 106 "   -0.044 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 106 "   -0.058 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 106 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 106 "   -0.049 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 106 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 106 "   -0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 106 "    0.030 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 106 "    0.035 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 106 "   -0.041 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 106 "   -0.071 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 106 "    0.041 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 106 "   -0.003 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 106 "    0.073 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 179 "   -0.129 2.00e-02 2.50e+03   6.01e-02 1.08e+02
        pdb=" CG  TYR B 179 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 179 "    0.044 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 179 "    0.041 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 179 "    0.037 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 179 "    0.044 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 179 "    0.017 2.00e-02 2.50e+03
        pdb=" OH  TYR B 179 "   -0.135 2.00e-02 2.50e+03
        pdb=" HD1 TYR B 179 "    0.018 2.00e-02 2.50e+03
        pdb=" HD2 TYR B 179 "    0.014 2.00e-02 2.50e+03
        pdb=" HE1 TYR B 179 "    0.016 2.00e-02 2.50e+03
        pdb=" HE2 TYR B 179 "    0.016 2.00e-02 2.50e+03
  ... (remaining 2126 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.17: 564
        2.17 -     2.78: 24825
        2.78 -     3.39: 42225
        3.39 -     3.99: 57740
        3.99 -     4.60: 81254
  Nonbonded interactions: 206608
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 264 "
            pdb=" HG  SER B 516 "
     model   vdw
     1.565 2.450
  nonbonded pdb=" OE2 GLU A 264 "
            pdb=" HG  SER A 516 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" OE2 GLU B 395 "
            pdb=" HG  SER B 419 "
     model   vdw
     1.628 2.450
  nonbonded pdb=" OE1 GLU A 320 "
            pdb=" HH  TYR A 499 "
     model   vdw
     1.632 2.450
  nonbonded pdb=" HG  SER B 392 "
            pdb=" OE1 GLU B 395 "
     model   vdw
     1.636 2.450
  ... (remaining 206603 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 14 through 487 or resid 491 through 566 or resid 901))
}

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:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.260
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.130
  Set scattering table:                    0.150
  Process input model:                     33.190
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
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      :  0.013   0.044   7468  Z= 0.845
  Angle     :  1.816   7.868  10153  Z= 1.266
  Chirality :  0.091   0.387   1198
  Planarity :  0.013   0.150   1243
  Dihedral  : 13.070  83.216   2599
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 0.13
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.51 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  2.09 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.11 %
  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: -0.45 (0.24), residues: 918
  helix: -0.07 (0.17), residues: 678
  sheet:  None (None), residues: 0
  loop : -0.53 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.098   0.016   TRP A 106 
 HIS   0.017   0.006   HIS B 210 
 PHE   0.084   0.015   PHE B  93 
 TYR   0.127   0.015   TYR B 179 
 ARG   0.008   0.001   ARG A 343 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7321 (mtm180) cc_final: 0.7110 (mtm180)
REVERT: A  167 MET cc_start: 0.8493 (mmm) cc_final: 0.8207 (mmm)
REVERT: A  178 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7051 (mm-30)
REVERT: A  404 ARG cc_start: 0.8549 (mmm160) cc_final: 0.7683 (mmm160)
REVERT: A  422 GLN cc_start: 0.6820 (mm110) cc_final: 0.5753 (mp10)
REVERT: A  441 MET cc_start: 0.8322 (mmp) cc_final: 0.8119 (mmm)
REVERT: A  471 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.6091 (mmt-90)
REVERT: A  535 MET cc_start: 0.8024 (mtp) cc_final: 0.7759 (mtp)
REVERT: B  101 MET cc_start: 0.8164 (tpt) cc_final: 0.7602 (tpt)
REVERT: B  117 GLN cc_start: 0.7180 (mt0) cc_final: 0.6920 (mp10)
REVERT: B  273 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.7000 (ttp-110)
REVERT: B  344 LYS cc_start: 0.8351 (tptt) cc_final: 0.8133 (mmmm)
REVERT: B  349 MET cc_start: 0.7592 (ppp) cc_final: 0.7211 (mtt)
REVERT: B  363 ARG cc_start: 0.6483 (mmm160) cc_final: 0.5952 (tpp80)
REVERT: B  369 LEU cc_start: 0.8395 (mt) cc_final: 0.8041 (mp)
REVERT: B  383 PHE cc_start: 0.8692 (t80) cc_final: 0.8469 (t80)
REVERT: B  404 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7402 (mtm-85)
REVERT: B  441 MET cc_start: 0.8226 (mmm) cc_final: 0.7972 (mmm)
REVERT: B  445 MET cc_start: 0.8531 (mtt) cc_final: 0.7916 (mtt)
REVERT: B  450 THR cc_start: 0.7915 (m) cc_final: 0.7404 (p)
REVERT: B  477 MET cc_start: 0.7944 (mmm) cc_final: 0.7744 (mmm)
REVERT: B  558 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7830 (mtm110)
  outliers start: 7
  outliers final: 2
  residues processed: 124
  average time/residue: 3.0769
  time to fit residues: 401.7104
Evaluate side-chains
  99 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  486 HIS
Chi-restraints excluded: chain A residue  521 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 153 GLN
B 422 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7468  Z= 0.246
  Angle     :  0.651   7.504  10153  Z= 0.365
  Chirality :  0.039   0.134   1198
  Planarity :  0.005   0.053   1243
  Dihedral  :  5.317  45.178   1005
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  5.24 %
    Favored  : 93.32 %
  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:  1.44 (0.26), residues: 918
  helix:  1.71 (0.19), residues: 684
  sheet: -0.21 (1.19), residues: 18
  loop : -1.41 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 121 
 HIS   0.007   0.002   HIS A 513 
 PHE   0.020   0.002   PHE A 459 
 TYR   0.014   0.002   TYR A 275 
 ARG   0.004   0.000   ARG A 277 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7328 (mtm180) cc_final: 0.6998 (mtm-85)
REVERT: A  101 MET cc_start: 0.7696 (tpt) cc_final: 0.7017 (tpt)
REVERT: A  167 MET cc_start: 0.8493 (mmm) cc_final: 0.8285 (mmm)
REVERT: A  314 PHE cc_start: 0.7294 (m-80) cc_final: 0.6991 (m-80)
REVERT: A  348 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7836 (t)
REVERT: A  404 ARG cc_start: 0.8376 (mmm160) cc_final: 0.7695 (mmm160)
REVERT: A  535 MET cc_start: 0.7746 (mtp) cc_final: 0.7520 (mtp)
REVERT: B  101 MET cc_start: 0.7911 (tpt) cc_final: 0.7687 (tpt)
REVERT: B  117 GLN cc_start: 0.7000 (mt0) cc_final: 0.6713 (mp10)
REVERT: B  167 MET cc_start: 0.8331 (mmm) cc_final: 0.8082 (mmp)
REVERT: B  273 ARG cc_start: 0.7293 (mtp-110) cc_final: 0.7017 (ttt-90)
REVERT: B  314 PHE cc_start: 0.7944 (m-80) cc_final: 0.7740 (m-80)
REVERT: B  349 MET cc_start: 0.7559 (ppp) cc_final: 0.6883 (mmp)
REVERT: B  450 THR cc_start: 0.7722 (m) cc_final: 0.7254 (p)
REVERT: B  477 MET cc_start: 0.7773 (mmm) cc_final: 0.7518 (mmm)
REVERT: B  486 HIS cc_start: 0.5058 (OUTLIER) cc_final: 0.4017 (p90)
REVERT: B  558 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7322 (mtm180)
  outliers start: 11
  outliers final: 3
  residues processed: 112
  average time/residue: 2.8242
  time to fit residues: 335.1331
Evaluate side-chains
  101 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  486 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  486 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 422 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7468  Z= 0.298
  Angle     :  0.623   6.677  10153  Z= 0.344
  Chirality :  0.041   0.145   1198
  Planarity :  0.006   0.050   1243
  Dihedral  :  4.839  36.430   1001
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  6.94 %
    Favored  : 91.23 %
  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:  1.51 (0.27), residues: 918
  helix:  1.81 (0.19), residues: 684
  sheet:  0.03 (1.20), residues: 18
  loop : -1.60 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 444 
 HIS   0.004   0.002   HIS A 530 
 PHE   0.023   0.002   PHE B 463 
 TYR   0.013   0.002   TYR A 275 
 ARG   0.007   0.001   ARG B 471 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.7442 (tpt) cc_final: 0.6980 (tpt)
REVERT: A  167 MET cc_start: 0.8471 (mmm) cc_final: 0.8257 (mmm)
REVERT: A  172 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7538 (mtm-85)
REVERT: A  273 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7658 (mtp180)
REVERT: A  277 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7766 (mtp85)
REVERT: A  349 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6633 (mpt)
REVERT: A  351 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7476 (mttp)
REVERT: A  404 ARG cc_start: 0.8381 (mmm160) cc_final: 0.7620 (mmm160)
REVERT: A  535 MET cc_start: 0.7803 (mtp) cc_final: 0.7554 (mtp)
REVERT: B  117 GLN cc_start: 0.6913 (mt0) cc_final: 0.6644 (mp10)
REVERT: B  166 GLU cc_start: 0.8507 (mp0) cc_final: 0.7803 (mp0)
REVERT: B  167 MET cc_start: 0.8308 (mmm) cc_final: 0.8003 (mmp)
REVERT: B  314 PHE cc_start: 0.7964 (m-80) cc_final: 0.7749 (m-80)
REVERT: B  349 MET cc_start: 0.7491 (ppp) cc_final: 0.6940 (mmp)
REVERT: B  395 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7306 (mt-10)
REVERT: B  404 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7331 (mmp-170)
REVERT: B  450 THR cc_start: 0.7858 (m) cc_final: 0.7334 (p)
REVERT: B  477 MET cc_start: 0.7758 (mmm) cc_final: 0.7508 (mmm)
REVERT: B  486 HIS cc_start: 0.5107 (OUTLIER) cc_final: 0.4185 (p90)
REVERT: B  558 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7448 (mtp180)
  outliers start: 14
  outliers final: 4
  residues processed: 104
  average time/residue: 2.9708
  time to fit residues: 327.4428
Evaluate side-chains
  106 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 1.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  273 ARG
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  486 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  486 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 422 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7468  Z= 0.171
  Angle     :  0.514   6.685  10153  Z= 0.280
  Chirality :  0.036   0.123   1198
  Planarity :  0.005   0.050   1243
  Dihedral  :  4.516  36.101   1001
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  7.33 %
    Favored  : 91.23 %
  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:  2.11 (0.27), residues: 918
  helix:  2.30 (0.19), residues: 683
  sheet:  0.07 (1.28), residues: 18
  loop : -1.57 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 444 
 HIS   0.002   0.001   HIS A 513 
 PHE   0.012   0.001   PHE B 463 
 TYR   0.008   0.001   TYR A 275 
 ARG   0.002   0.000   ARG B 471 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.7352 (tpt) cc_final: 0.6989 (tpt)
REVERT: A  273 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7448 (ptm-80)
REVERT: A  314 PHE cc_start: 0.7371 (m-80) cc_final: 0.7069 (m-80)
REVERT: A  349 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6518 (mpt)
REVERT: A  351 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7258 (mttp)
REVERT: A  404 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7573 (mmm160)
REVERT: A  535 MET cc_start: 0.7682 (mtp) cc_final: 0.7400 (mtp)
REVERT: B  117 GLN cc_start: 0.6818 (mt0) cc_final: 0.6538 (mp10)
REVERT: B  166 GLU cc_start: 0.8450 (mp0) cc_final: 0.8078 (mp0)
REVERT: B  167 MET cc_start: 0.8309 (mmm) cc_final: 0.8056 (mmp)
REVERT: B  238 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7253 (tt0)
REVERT: B  273 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.7224 (ttt-90)
REVERT: B  349 MET cc_start: 0.7454 (ppp) cc_final: 0.6889 (mmp)
REVERT: B  404 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7294 (mmp-170)
REVERT: B  450 THR cc_start: 0.7778 (m) cc_final: 0.7303 (p)
REVERT: B  477 MET cc_start: 0.7707 (mmm) cc_final: 0.7501 (mmm)
REVERT: B  486 HIS cc_start: 0.5094 (OUTLIER) cc_final: 0.4078 (p90)
REVERT: B  558 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7424 (mtp180)
  outliers start: 11
  outliers final: 2
  residues processed: 107
  average time/residue: 2.9566
  time to fit residues: 333.9684
Evaluate side-chains
  104 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 ARG
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  486 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  486 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 422 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7468  Z= 0.347
  Angle     :  0.620   5.894  10153  Z= 0.343
  Chirality :  0.042   0.147   1198
  Planarity :  0.006   0.050   1243
  Dihedral  :  4.687  34.305   1001
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  7.33 %
    Favored  : 90.84 %
  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:  1.69 (0.27), residues: 918
  helix:  1.99 (0.19), residues: 682
  sheet:  0.00 (1.25), residues: 18
  loop : -1.68 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 444 
 HIS   0.003   0.001   HIS B 513 
 PHE   0.022   0.002   PHE B 463 
 TYR   0.013   0.002   TYR A 275 
 ARG   0.005   0.001   ARG A 471 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 1.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7450 (tt0) cc_final: 0.6904 (tm-30)
REVERT: A  349 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6568 (mpt)
REVERT: A  351 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7422 (mttp)
REVERT: A  369 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7843 (mp)
REVERT: A  404 ARG cc_start: 0.8408 (mmm160) cc_final: 0.7625 (mmm160)
REVERT: A  535 MET cc_start: 0.7754 (mtp) cc_final: 0.7507 (mtp)
REVERT: B  117 GLN cc_start: 0.6994 (mt0) cc_final: 0.6714 (mp10)
REVERT: B  166 GLU cc_start: 0.8468 (mp0) cc_final: 0.7730 (mp0)
REVERT: B  167 MET cc_start: 0.8292 (mmm) cc_final: 0.7989 (mmp)
REVERT: B  349 MET cc_start: 0.7537 (ppp) cc_final: 0.6976 (mmp)
REVERT: B  404 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7360 (mmp-170)
REVERT: B  450 THR cc_start: 0.7796 (m) cc_final: 0.7233 (p)
REVERT: B  486 HIS cc_start: 0.5132 (OUTLIER) cc_final: 0.4189 (p90)
REVERT: B  558 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7462 (mtp180)
  outliers start: 14
  outliers final: 4
  residues processed: 104
  average time/residue: 3.2363
  time to fit residues: 354.9333
Evaluate side-chains
  105 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  486 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  486 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 422 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7468  Z= 0.179
  Angle     :  0.522   6.869  10153  Z= 0.283
  Chirality :  0.036   0.123   1198
  Planarity :  0.005   0.050   1243
  Dihedral  :  4.441  34.467   1001
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  7.98 %
    Favored  : 90.58 %
  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:  2.18 (0.27), residues: 918
  helix:  2.40 (0.19), residues: 682
  sheet:  0.03 (1.27), residues: 18
  loop : -1.69 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 121 
 HIS   0.002   0.001   HIS B 210 
 PHE   0.015   0.001   PHE B 463 
 TYR   0.009   0.001   TYR A 275 
 ARG   0.002   0.000   ARG A 311 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7439 (tt0) cc_final: 0.6870 (tm-30)
REVERT: A  349 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6468 (mpt)
REVERT: A  351 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7372 (mttp)
REVERT: A  369 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7789 (mp)
REVERT: A  404 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7603 (mmm160)
REVERT: B  117 GLN cc_start: 0.6792 (mt0) cc_final: 0.6505 (mp10)
REVERT: B  166 GLU cc_start: 0.8461 (mp0) cc_final: 0.7691 (mp0)
REVERT: B  167 MET cc_start: 0.8272 (mmm) cc_final: 0.7999 (mmp)
REVERT: B  238 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7108 (tt0)
REVERT: B  349 MET cc_start: 0.7569 (ppp) cc_final: 0.7008 (mmp)
REVERT: B  404 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7314 (mmp-170)
REVERT: B  450 THR cc_start: 0.7823 (m) cc_final: 0.7277 (p)
REVERT: B  486 HIS cc_start: 0.5077 (OUTLIER) cc_final: 0.4068 (p90)
REVERT: B  558 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7426 (mtp180)
  outliers start: 11
  outliers final: 2
  residues processed: 105
  average time/residue: 3.2523
  time to fit residues: 360.6001
Evaluate side-chains
  104 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  486 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  486 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 56 optimal weight:    0.1980
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 422 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7468  Z= 0.212
  Angle     :  0.525   6.143  10153  Z= 0.285
  Chirality :  0.037   0.133   1198
  Planarity :  0.005   0.052   1243
  Dihedral  :  4.374  33.761   1001
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  7.72 %
    Favored  : 90.58 %
  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:  2.23 (0.27), residues: 918
  helix:  2.47 (0.19), residues: 682
  sheet: -0.10 (1.20), residues: 18
  loop : -1.76 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 121 
 HIS   0.002   0.001   HIS B 210 
 PHE   0.017   0.001   PHE B 463 
 TYR   0.010   0.001   TYR A 275 
 ARG   0.002   0.000   ARG A 471 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7434 (tt0) cc_final: 0.6860 (tm-30)
REVERT: A  349 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6408 (mpt)
REVERT: A  351 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7343 (mttp)
REVERT: A  369 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7816 (mp)
REVERT: A  404 ARG cc_start: 0.8375 (mmm160) cc_final: 0.7612 (mmm160)
REVERT: B  117 GLN cc_start: 0.6861 (mt0) cc_final: 0.6593 (mp10)
REVERT: B  166 GLU cc_start: 0.8419 (mp0) cc_final: 0.7711 (mp0)
REVERT: B  167 MET cc_start: 0.8282 (mmm) cc_final: 0.7975 (mmp)
REVERT: B  349 MET cc_start: 0.7585 (ppp) cc_final: 0.7035 (mmp)
REVERT: B  363 ARG cc_start: 0.6782 (mmm160) cc_final: 0.5868 (tpp80)
REVERT: B  395 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7292 (mt-10)
REVERT: B  404 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7325 (mmp-170)
REVERT: B  450 THR cc_start: 0.7804 (m) cc_final: 0.7240 (p)
REVERT: B  486 HIS cc_start: 0.5123 (OUTLIER) cc_final: 0.4265 (p90)
REVERT: B  558 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7486 (mtp180)
  outliers start: 13
  outliers final: 3
  residues processed: 108
  average time/residue: 3.3578
  time to fit residues: 381.9691
Evaluate side-chains
  109 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 1.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  486 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  486 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 422 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7468  Z= 0.281
  Angle     :  0.571   5.898  10153  Z= 0.312
  Chirality :  0.039   0.141   1198
  Planarity :  0.006   0.052   1243
  Dihedral  :  4.503  33.667   1001
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.64 %
    Favored  : 90.05 %
  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:  2.04 (0.27), residues: 918
  helix:  2.30 (0.19), residues: 682
  sheet: -0.14 (1.19), residues: 18
  loop : -1.75 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 121 
 HIS   0.002   0.001   HIS B 513 
 PHE   0.019   0.002   PHE B 463 
 TYR   0.012   0.001   TYR A 275 
 ARG   0.006   0.000   ARG A 273 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7435 (tt0) cc_final: 0.6864 (tm-30)
REVERT: A  238 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7267 (mt-10)
REVERT: A  349 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6485 (mpt)
REVERT: A  351 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7353 (mttp)
REVERT: A  369 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7850 (mp)
REVERT: A  404 ARG cc_start: 0.8391 (mmm160) cc_final: 0.7632 (mmm160)
REVERT: B  117 GLN cc_start: 0.6803 (mt0) cc_final: 0.6577 (mp10)
REVERT: B  166 GLU cc_start: 0.8419 (mp0) cc_final: 0.8046 (mp0)
REVERT: B  167 MET cc_start: 0.8267 (mmm) cc_final: 0.7935 (mmp)
REVERT: B  349 MET cc_start: 0.7595 (ppp) cc_final: 0.7035 (mmp)
REVERT: B  363 ARG cc_start: 0.6821 (mmm160) cc_final: 0.5902 (tpp80)
REVERT: B  404 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7345 (mmp-170)
REVERT: B  450 THR cc_start: 0.7810 (m) cc_final: 0.7248 (p)
REVERT: B  486 HIS cc_start: 0.5096 (OUTLIER) cc_final: 0.4247 (p90)
REVERT: B  558 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7512 (mtp180)
  outliers start: 10
  outliers final: 3
  residues processed: 107
  average time/residue: 3.1195
  time to fit residues: 352.3073
Evaluate side-chains
  109 residues out of total 764 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  486 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  486 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0570
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.1500

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

Flipped N/Q/H residues before XYZ refinement:
B 422 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3109
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_fail.pdb'.
Return code: -15
Dumping stderr: