Starting phenix.real_space_refine
on Fri Jul 25 16:09:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vk3_21224/07_2025/6vk3_21224.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vk3_21224/07_2025/6vk3_21224.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vk3_21224/07_2025/6vk3_21224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vk3_21224/07_2025/6vk3_21224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vk3_21224/07_2025/6vk3_21224.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vk3_21224/07_2025/6vk3_21224.cif"
  }
  resolution = 3.7
  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=   0.000 sd=   0.005
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      38      5.16       5
     C    4967      2.51       5
     N    1303      2.21       5
     O    1476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7784
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1906
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 3060
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3060
          Classifications: {'peptide': 381}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 11, 'TRANS': 369}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'UNK:plan-1': 7}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2818
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 10, 'TRANS': 339}
          Chain breaks: 2
  Time building chain proxies: 4.98, per 1000 atoms: 0.64
  Number of scatterers: 7784
  At special positions: 0
  Unit cell: (103.88, 101.76, 103.88, 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      38     16.00
     O    1476      8.00
     N    1303      7.00
     C    4967      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  70 " - pdb=" SG  CYS B 258 " distance=2.81
    Simple disulfide: pdb=" SG  CYS B 117 " - pdb=" SG  CYS B 130 " distance=2.50
    Simple disulfide: pdb=" SG  CYS B 193 " - pdb=" SG  CYS B 227 " distance=2.87
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS B 239 " distance=2.21

  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: 2.15
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      55.3% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 42 through 47
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 83 through 100
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 124 through 139
    Processing helix  chain 'A' and resid 142 through 156
    Processing helix  chain 'A' and resid 170 through 184
      removed outlier: 3.612A  pdb=" N   ALA A 174 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 200
    Processing helix  chain 'A' and resid 206 through 225
      removed outlier: 3.604A  pdb=" N   TYR A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
    Processing helix  chain 'A' and resid 314 through 331
      removed outlier: 4.074A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 326 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 356 through 358
      No H-bonds generated for 'chain 'A' and resid 356 through 358'
    Processing helix  chain 'A' and resid 362 through 383
    Processing helix  chain 'A' and resid 390 through 407
    Processing helix  chain 'A' and resid 412 through 423
    Processing helix  chain 'A' and resid 429 through 442
      removed outlier: 4.813A  pdb=" N   LYS A 442 " --> pdb=" O   MET A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 462 through 465
      removed outlier: 3.907A  pdb=" N   LYS A 465 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 462 through 465'
    Processing helix  chain 'A' and resid 468 through 480
    Processing helix  chain 'A' and resid 481 through 494
      removed outlier: 3.615A  pdb=" N   TYR A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 4.190A  pdb=" N   GLU A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 4.119A  pdb=" N   THR A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 550
      removed outlier: 3.539A  pdb=" N   LEU A 540 " --> pdb=" O   SER A 536 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLU A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLN A 549 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.874A  pdb=" N   SER A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 609
      removed outlier: 4.113A  pdb=" N   GLY A 599 " --> pdb=" O   ASN A 595 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL A 600 " --> pdb=" O   ILE A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 624
      removed outlier: 3.750A  pdb=" N   ALA A 617 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 640
      removed outlier: 3.516A  pdb=" N   HIS A 640 " --> pdb=" O   TYR A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 662
      removed outlier: 3.714A  pdb=" N   ASP A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 684
    Processing helix  chain 'B' and resid 41 through 49
      removed outlier: 3.637A  pdb=" N   ILE B  49 " --> pdb=" O   TRP B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 58
      removed outlier: 3.785A  pdb=" N   MET B  56 " --> pdb=" O   ASN B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 114
    Processing helix  chain 'B' and resid 236 through 245
      removed outlier: 3.524A  pdb=" N   ASN B 240 " --> pdb=" O   GLU B 237 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   GLU B 242 " --> pdb=" O   CYS B 239 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU B 243 " --> pdb=" O   ASN B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 276
    Processing helix  chain 'B' and resid 314 through 332
      removed outlier: 3.688A  pdb=" N   TYR B 318 " --> pdb=" O   THR B 314 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62
      removed outlier: 7.068A  pdb=" N   VAL A  61 " --> pdb=" O   UNK A 291 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 40
      removed outlier: 6.193A  pdb=" N   LEU B  36 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   CYS B 258 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   SER B  38 " --> pdb=" O   CYS B 258 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 122
      removed outlier: 3.962A  pdb=" N   VAL B 136 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 176
      removed outlier: 8.895A  pdb=" N   TYR B 181 " --> pdb=" O   CYS B 208 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   CYS B 208 " --> pdb=" O   TYR B 181 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TYR B 229 " --> pdb=" O   MET B 201 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   TRP B 220 " --> pdb=" O   GLN B 232 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   THR B 234 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   ILE B 218 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 277 through 278
      removed outlier: 3.528A  pdb=" N   ARG B 290 " --> pdb=" O   GLU B 278 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   THR B 363 " --> pdb=" O   VAL B 354 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ASN B 368 " --> pdb=" O   GLU B 376 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   GLU B 376 " --> pdb=" O   ASN B 368 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 277 through 278
      removed outlier: 3.528A  pdb=" N   ARG B 290 " --> pdb=" O   GLU B 278 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER B 347 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.20

  Time building geometry restraints manager: 2.51 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: 2453
        1.34 -     1.46: 1438
        1.46 -     1.58: 4006
        1.58 -     1.70: 0
        1.70 -     1.82: 63
  Bond restraints: 7960
  Sorted by residual:
  bond pdb=" C   ARG B 116 "
       pdb=" N   CYS B 117 "
    ideal  model  delta    sigma   weight residual
    1.330  1.235  0.095 1.38e-02 5.25e+03 4.71e+01
  bond pdb=" C   CYS B 117 "
       pdb=" N   ILE B 118 "
    ideal  model  delta    sigma   weight residual
    1.333  1.248  0.085 1.34e-02 5.57e+03 4.04e+01
  bond pdb=" CE1 HIS B 139 "
       pdb=" NE2 HIS B 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.25e+00
  bond pdb=" N   VAL B 179 "
       pdb=" CA  VAL B 179 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.035 1.19e-02 7.06e+03 8.57e+00
  bond pdb=" N   TYR B 181 "
       pdb=" CA  TYR B 181 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.31e-02 5.83e+03 8.52e+00
  ... (remaining 7955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 10108
        1.86 -     3.72: 557
        3.72 -     5.58: 84
        5.58 -     7.44: 21
        7.44 -     9.30: 1
  Bond angle restraints: 10771
  Sorted by residual:
  angle pdb=" N   LEU B  68 "
        pdb=" CA  LEU B  68 "
        pdb=" C   LEU B  68 "
      ideal   model   delta    sigma   weight residual
     112.41  105.55    6.86 1.30e+00 5.92e-01 2.79e+01
  angle pdb=" C   LEU B 241 "
        pdb=" N   GLU B 242 "
        pdb=" CA  GLU B 242 "
      ideal   model   delta    sigma   weight residual
     120.54  126.97   -6.43 1.35e+00 5.49e-01 2.27e+01
  angle pdb=" CA  ASN B 166 "
        pdb=" CB  ASN B 166 "
        pdb=" CG  ASN B 166 "
      ideal   model   delta    sigma   weight residual
     112.60  117.34   -4.74 1.00e+00 1.00e+00 2.25e+01
  angle pdb=" C   CYS B 130 "
        pdb=" N   PRO B 131 "
        pdb=" CA  PRO B 131 "
      ideal   model   delta    sigma   weight residual
     119.84  125.42   -5.58 1.25e+00 6.40e-01 1.99e+01
  angle pdb=" N   GLU B 242 "
        pdb=" CA  GLU B 242 "
        pdb=" CB  GLU B 242 "
      ideal   model   delta    sigma   weight residual
     109.94  103.38    6.56 1.49e+00 4.50e-01 1.94e+01
  ... (remaining 10766 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.84: 4189
       16.84 -    33.68: 446
       33.68 -    50.52: 98
       50.52 -    67.36: 18
       67.36 -    84.21: 14
  Dihedral angle restraints: 4765
    sinusoidal: 1921
      harmonic: 2844
  Sorted by residual:
  dihedral pdb=" CA  ASN A 516 "
           pdb=" C   ASN A 516 "
           pdb=" N   GLU A 517 "
           pdb=" CA  GLU A 517 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.64   24.36     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CB  CYS B 208 "
           pdb=" SG  CYS B 208 "
           pdb=" SG  CYS B 239 "
           pdb=" CB  CYS B 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.09   39.09     1      1.00e+01 1.00e-02 2.15e+01
  dihedral pdb=" CA  ASN A 533 "
           pdb=" C   ASN A 533 "
           pdb=" N   ASP A 534 "
           pdb=" CA  ASP A 534 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.45   21.55     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 4762 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 949
       0.065 -    0.129: 165
       0.129 -    0.194: 39
       0.194 -    0.259: 5
       0.259 -    0.324: 2
  Chirality restraints: 1160
  Sorted by residual:
  chirality pdb=" CB  THR B 224 "
            pdb=" CA  THR B 224 "
            pdb=" OG1 THR B 224 "
            pdb=" CG2 THR B 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.23    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  ARG B 116 "
            pdb=" N   ARG B 116 "
            pdb=" C   ARG B 116 "
            pdb=" CB  ARG B 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CB  THR B 196 "
            pdb=" CA  THR B 196 "
            pdb=" OG1 THR B 196 "
            pdb=" CG2 THR B 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1157 not shown)

  Planarity restraints: 1384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 125 "    0.209 2.00e-02 2.50e+03   1.05e-01 2.77e+02
        pdb=" CG  TRP B 125 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 125 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 125 "   -0.112 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 125 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 125 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 125 "   -0.135 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 125 "    0.119 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 125 "   -0.037 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 125 "    0.118 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 129 "    0.077 2.00e-02 2.50e+03   4.94e-02 4.88e+01
        pdb=" CG  TYR B 129 "    0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 129 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 129 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 129 "   -0.043 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 129 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 129 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR B 129 "    0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 110 "   -0.048 2.00e-02 2.50e+03   3.06e-02 1.63e+01
        pdb=" CG  PHE B 110 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 110 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 110 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 110 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 110 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 110 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1381 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 78
        2.59 -     3.17: 6732
        3.17 -     3.75: 11739
        3.75 -     4.32: 15926
        4.32 -     4.90: 26692
  Nonbonded interactions: 61167
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 309 "
            pdb=" OD1 ASN B 309 "
     model   vdw
     2.013 3.040
  nonbonded pdb=" NE2 GLN B 250 "
            pdb=" ND2 ASN B 252 "
     model   vdw
     2.245 3.200
  nonbonded pdb=" OG  SER A  97 "
            pdb=" OG1 THR A 106 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OD1 ASP A 231 "
            pdb=" NZ  LYS A 456 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" CB  PRO B  25 "
            pdb=" OH  TYR B 176 "
     model   vdw
     2.307 3.440
  ... (remaining 61162 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:             0.450
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     21.660
  Find NCS groups from input model:        0.070
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
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      :  0.015   0.834   7964  Z= 0.766
  Angle     :  0.999  29.627  10779  Z= 0.611
  Chirality :  0.056   0.324   1160
  Planarity :  0.007   0.105   1384
  Dihedral  : 14.845  84.206   2925
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.11 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  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: -2.61 (0.24), residues: 940
  helix: -0.92 (0.20), residues: 499
  sheet: -1.96 (0.59), residues: 74
  loop : -2.76 (0.28), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.209   0.008   TRP B 125 
 HIS   0.008   0.001   HIS B 139 
 PHE   0.048   0.004   PHE B 110 
 TYR   0.086   0.002   TYR B 129 
 ARG   0.009   0.000   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14596 (  405)
  hydrogen bonds       : angle       6.45916 ( 1206)
  SS BOND              : bond        0.62244 (    4)
  SS BOND              : angle      13.03753 (    8)
  covalent geometry    : bond        0.00599 ( 7960)
  covalent geometry    : angle       0.93391 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.8370 (m-30) cc_final: 0.8134 (m-30)
REVERT: A  238 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8006 (mp0)
REVERT: A  670 LYS cc_start: 0.6744 (mmtt) cc_final: 0.6488 (mmtt)
REVERT: A  675 LYS cc_start: 0.8677 (tptm) cc_final: 0.7923 (tmmt)
REVERT: B   64 MET cc_start: 0.8875 (mmt) cc_final: 0.8591 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.2484
  time to fit residues: 46.0263
Evaluate side-chains
  98 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 202 ASN
A 208 HIS
B 121 GLN
B 326 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.194062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.144322 restraints weight = 9896.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.141604 restraints weight = 9781.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.143612 restraints weight = 9584.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7964  Z= 0.150
  Angle     :  0.557   6.825  10779  Z= 0.298
  Chirality :  0.041   0.146   1160
  Planarity :  0.003   0.043   1384
  Dihedral  :  4.464  22.358   1060
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.91 %
    Favored  : 83.83 %
  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: -1.00 (0.26), residues: 940
  helix:  0.54 (0.23), residues: 501
  sheet: -1.76 (0.51), residues: 91
  loop : -2.11 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 125 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 201 
 TYR   0.010   0.001   TYR B 182 
 ARG   0.004   0.000   ARG B 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04127 (  405)
  hydrogen bonds       : angle       4.62682 ( 1206)
  SS BOND              : bond        0.00486 (    4)
  SS BOND              : angle       0.87379 (    8)
  covalent geometry    : bond        0.00334 ( 7960)
  covalent geometry    : angle       0.55631 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 1.526 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.8344 (m-30) cc_final: 0.8110 (m-30)
REVERT: A  184 LEU cc_start: 0.9394 (mt) cc_final: 0.9067 (mt)
REVERT: A  347 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8457 (mm)
REVERT: A  639 GLU cc_start: 0.8830 (pp20) cc_final: 0.8075 (pt0)
REVERT: A  670 LYS cc_start: 0.6884 (mmtt) cc_final: 0.6332 (mmtt)
REVERT: B   39 TYR cc_start: 0.8205 (m-80) cc_final: 0.7996 (m-10)
REVERT: B   64 MET cc_start: 0.8956 (mmt) cc_final: 0.8724 (mmp)
REVERT: B  278 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8283 (tm-30)
  outliers start: 19
  outliers final: 9
  residues processed: 139
  average time/residue: 0.2128
  time to fit residues: 40.9254
Evaluate side-chains
  115 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 95 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 202 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.194182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.143504 restraints weight = 9915.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.140287 restraints weight = 9417.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.142475 restraints weight = 9068.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7964  Z= 0.147
  Angle     :  0.524   9.708  10779  Z= 0.276
  Chirality :  0.039   0.139   1160
  Planarity :  0.003   0.041   1384
  Dihedral  :  4.296  21.654   1060
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.12 %
    Favored  : 79.79 %
  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: -0.43 (0.27), residues: 940
  helix:  1.05 (0.23), residues: 504
  sheet: -1.60 (0.55), residues: 84
  loop : -1.94 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 541 
 HIS   0.002   0.001   HIS A 128 
 PHE   0.011   0.001   PHE A 367 
 TYR   0.009   0.001   TYR A 368 
 ARG   0.002   0.000   ARG B 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03855 (  405)
  hydrogen bonds       : angle       4.35347 ( 1206)
  SS BOND              : bond        0.00163 (    4)
  SS BOND              : angle       0.62826 (    8)
  covalent geometry    : bond        0.00335 ( 7960)
  covalent geometry    : angle       0.52375 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8028 (mm-40)
REVERT: A  347 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8420 (mm)
REVERT: A  611 ASN cc_start: 0.7449 (t0) cc_final: 0.7225 (m-40)
REVERT: A  670 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6364 (mmtt)
REVERT: B   39 TYR cc_start: 0.8263 (m-80) cc_final: 0.8057 (m-80)
REVERT: B   64 MET cc_start: 0.8965 (mmt) cc_final: 0.8670 (mmt)
REVERT: B  175 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.6005 (mp)
REVERT: B  278 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8330 (tm-30)
REVERT: B  287 TYR cc_start: 0.9115 (m-80) cc_final: 0.8859 (m-80)
  outliers start: 26
  outliers final: 14
  residues processed: 136
  average time/residue: 0.2140
  time to fit residues: 40.8806
Evaluate side-chains
  123 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 73 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0040
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 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 = 0.4140 r_free = 0.4140 target = 0.196174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.144638 restraints weight = 9826.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.141876 restraints weight = 9567.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.143884 restraints weight = 8969.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7964  Z= 0.122
  Angle     :  0.498   7.856  10779  Z= 0.263
  Chirality :  0.039   0.133   1160
  Planarity :  0.003   0.047   1384
  Dihedral  :  4.109  20.796   1060
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.36 %
    Favored  : 79.07 %
  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: -0.11 (0.27), residues: 940
  helix:  1.30 (0.23), residues: 505
  sheet: -1.33 (0.60), residues: 79
  loop : -1.83 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  45 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.009   0.001   PHE A 452 
 TYR   0.008   0.001   TYR A 368 
 ARG   0.002   0.000   ARG A 579 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  405)
  hydrogen bonds       : angle       4.19996 ( 1206)
  SS BOND              : bond        0.00149 (    4)
  SS BOND              : angle       0.59439 (    8)
  covalent geometry    : bond        0.00269 ( 7960)
  covalent geometry    : angle       0.49817 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7947 (mm-40)
REVERT: A  347 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8463 (mm)
REVERT: A  380 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.7996 (m-10)
REVERT: A  444 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7786 (tp40)
REVERT: A  611 ASN cc_start: 0.7508 (t0) cc_final: 0.7216 (m-40)
REVERT: A  670 LYS cc_start: 0.6697 (mmtt) cc_final: 0.6162 (mmtt)
REVERT: B   64 MET cc_start: 0.8916 (mmt) cc_final: 0.8649 (mmp)
REVERT: B  175 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6146 (mp)
REVERT: B  216 SER cc_start: 0.1822 (OUTLIER) cc_final: 0.0838 (t)
REVERT: B  278 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8298 (tm-30)
REVERT: B  287 TYR cc_start: 0.9128 (m-80) cc_final: 0.8838 (m-80)
  outliers start: 30
  outliers final: 15
  residues processed: 135
  average time/residue: 0.2477
  time to fit residues: 48.0338
Evaluate side-chains
  127 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 2.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.194635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.142936 restraints weight = 9853.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.140995 restraints weight = 9967.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.142679 restraints weight = 8933.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7964  Z= 0.146
  Angle     :  0.524  10.619  10779  Z= 0.273
  Chirality :  0.039   0.146   1160
  Planarity :  0.003   0.044   1384
  Dihedral  :  4.140  21.206   1060
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.43 %
    Favored  : 77.65 %
  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:  0.06 (0.28), residues: 940
  helix:  1.45 (0.23), residues: 504
  sheet: -1.29 (0.61), residues: 79
  loop : -1.74 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.009   0.001   PHE A 452 
 TYR   0.008   0.001   TYR A 368 
 ARG   0.003   0.000   ARG B 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03627 (  405)
  hydrogen bonds       : angle       4.21260 ( 1206)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       0.62392 (    8)
  covalent geometry    : bond        0.00330 ( 7960)
  covalent geometry    : angle       0.52416 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 114
  time to evaluate  : 1.475 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8812 (ttm) cc_final: 0.8422 (mtp)
REVERT: A  347 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8415 (mm)
REVERT: A  348 GLU cc_start: 0.7573 (tp30) cc_final: 0.7217 (tp30)
REVERT: A  380 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.7843 (m-10)
REVERT: A  444 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7840 (tp40)
REVERT: A  611 ASN cc_start: 0.7433 (t0) cc_final: 0.7153 (m-40)
REVERT: A  639 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8308 (tt0)
REVERT: A  670 LYS cc_start: 0.6788 (mmtt) cc_final: 0.6198 (mmtt)
REVERT: B   64 MET cc_start: 0.9019 (mmt) cc_final: 0.8731 (mmp)
REVERT: B  175 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.6074 (mp)
REVERT: B  216 SER cc_start: 0.2277 (OUTLIER) cc_final: 0.1316 (t)
REVERT: B  278 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8328 (tm-30)
  outliers start: 33
  outliers final: 21
  residues processed: 139
  average time/residue: 0.2096
  time to fit residues: 43.1083
Evaluate side-chains
  133 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 75 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0050
   chunk 86 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    0.2980
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.201538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.152098 restraints weight = 9821.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.152356 restraints weight = 9448.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.153877 restraints weight = 8090.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7964  Z= 0.113
  Angle     :  0.505   9.526  10779  Z= 0.261
  Chirality :  0.038   0.139   1160
  Planarity :  0.003   0.044   1384
  Dihedral  :  3.986  19.951   1060
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.26 %
    Favored  : 76.58 %
  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:  0.23 (0.28), residues: 940
  helix:  1.60 (0.23), residues: 504
  sheet: -1.24 (0.61), residues: 79
  loop : -1.67 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  45 
 HIS   0.002   0.001   HIS A 122 
 PHE   0.008   0.001   PHE A 452 
 TYR   0.008   0.001   TYR A  65 
 ARG   0.003   0.000   ARG B 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03346 (  405)
  hydrogen bonds       : angle       4.08636 ( 1206)
  SS BOND              : bond        0.00140 (    4)
  SS BOND              : angle       0.61446 (    8)
  covalent geometry    : bond        0.00248 ( 7960)
  covalent geometry    : angle       0.50452 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8792 (ttm) cc_final: 0.8437 (mtp)
REVERT: A  347 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8433 (mm)
REVERT: A  348 GLU cc_start: 0.7556 (tp30) cc_final: 0.7250 (tp30)
REVERT: A  380 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.7821 (m-10)
REVERT: A  390 ASN cc_start: 0.8725 (m-40) cc_final: 0.8442 (t0)
REVERT: A  428 ASN cc_start: 0.7355 (m-40) cc_final: 0.6571 (t0)
REVERT: A  444 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7816 (tp40)
REVERT: A  611 ASN cc_start: 0.7398 (t0) cc_final: 0.7137 (m-40)
REVERT: A  639 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8311 (tt0)
REVERT: B   51 GLN cc_start: 0.6722 (mm110) cc_final: 0.6412 (mm-40)
REVERT: B   64 MET cc_start: 0.9001 (mmt) cc_final: 0.8756 (mmp)
REVERT: B  175 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5996 (mp)
REVERT: B  216 SER cc_start: 0.2380 (OUTLIER) cc_final: 0.1423 (t)
REVERT: B  278 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8323 (tm-30)
  outliers start: 35
  outliers final: 22
  residues processed: 142
  average time/residue: 0.2040
  time to fit residues: 42.4972
Evaluate side-chains
  134 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  325 ILE
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 95 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.199405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.149564 restraints weight = 9829.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.148237 restraints weight = 10616.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.149431 restraints weight = 9024.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7964  Z= 0.136
  Angle     :  0.532   8.859  10779  Z= 0.273
  Chirality :  0.039   0.135   1160
  Planarity :  0.003   0.043   1384
  Dihedral  :  4.020  20.447   1060
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.86 %
    Favored  : 75.98 %
  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:  0.27 (0.28), residues: 940
  helix:  1.61 (0.23), residues: 505
  sheet: -1.20 (0.60), residues: 79
  loop : -1.62 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.010   0.001   PHE A 452 
 TYR   0.011   0.001   TYR A 368 
 ARG   0.003   0.000   ARG B 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03541 (  405)
  hydrogen bonds       : angle       4.13716 ( 1206)
  SS BOND              : bond        0.00155 (    4)
  SS BOND              : angle       0.71278 (    8)
  covalent geometry    : bond        0.00306 ( 7960)
  covalent geometry    : angle       0.53171 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 113
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8863 (ttm) cc_final: 0.8509 (mtp)
REVERT: A  183 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7986 (mm-40)
REVERT: A  347 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8466 (mm)
REVERT: A  348 GLU cc_start: 0.7636 (tp30) cc_final: 0.7324 (tp30)
REVERT: A  380 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.7813 (m-10)
REVERT: A  428 ASN cc_start: 0.7292 (m-40) cc_final: 0.6622 (t0)
REVERT: A  429 ASN cc_start: 0.7040 (t0) cc_final: 0.6827 (t0)
REVERT: A  444 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7834 (tp40)
REVERT: A  478 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9252 (mm)
REVERT: A  611 ASN cc_start: 0.7503 (t0) cc_final: 0.7201 (m-40)
REVERT: A  639 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8198 (tt0)
REVERT: B   64 MET cc_start: 0.9033 (mmt) cc_final: 0.8760 (mmp)
REVERT: B  201 MET cc_start: -0.1056 (mmp) cc_final: -0.1404 (mmp)
REVERT: B  216 SER cc_start: 0.2679 (OUTLIER) cc_final: 0.1740 (t)
  outliers start: 35
  outliers final: 23
  residues processed: 139
  average time/residue: 0.1805
  time to fit residues: 35.8505
Evaluate side-chains
  136 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 81 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 8 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 319 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.201086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.151918 restraints weight = 9893.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.152148 restraints weight = 10131.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.153898 restraints weight = 8158.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7964  Z= 0.118
  Angle     :  0.527   8.438  10779  Z= 0.271
  Chirality :  0.039   0.135   1160
  Planarity :  0.003   0.042   1384
  Dihedral  :  3.970  19.682   1060
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.69 %
    Favored  : 75.86 %
  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:  0.33 (0.28), residues: 940
  helix:  1.63 (0.23), residues: 505
  sheet: -1.12 (0.59), residues: 79
  loop : -1.57 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  45 
 HIS   0.002   0.001   HIS A 122 
 PHE   0.009   0.001   PHE B  71 
 TYR   0.010   0.001   TYR A 368 
 ARG   0.003   0.000   ARG B 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  405)
  hydrogen bonds       : angle       4.10492 ( 1206)
  SS BOND              : bond        0.00161 (    4)
  SS BOND              : angle       0.74377 (    8)
  covalent geometry    : bond        0.00263 ( 7960)
  covalent geometry    : angle       0.52667 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8857 (ttm) cc_final: 0.8480 (mtp)
REVERT: A  183 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7940 (mm-40)
REVERT: A  347 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8460 (mm)
REVERT: A  348 GLU cc_start: 0.7676 (tp30) cc_final: 0.7366 (tp30)
REVERT: A  380 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.7850 (m-10)
REVERT: A  428 ASN cc_start: 0.7040 (m-40) cc_final: 0.6571 (t0)
REVERT: A  429 ASN cc_start: 0.6835 (t0) cc_final: 0.6634 (t0)
REVERT: A  444 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7813 (tp40)
REVERT: A  478 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9230 (mm)
REVERT: A  611 ASN cc_start: 0.7360 (t0) cc_final: 0.7128 (m-40)
REVERT: A  639 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8278 (tt0)
REVERT: A  670 LYS cc_start: 0.6754 (mmtt) cc_final: 0.6272 (mptt)
REVERT: B   64 MET cc_start: 0.8979 (mmt) cc_final: 0.8665 (mmp)
REVERT: B  175 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6154 (mp)
REVERT: B  216 SER cc_start: 0.2696 (OUTLIER) cc_final: 0.1753 (t)
REVERT: B  309 ASN cc_start: 0.7586 (p0) cc_final: 0.7356 (p0)
  outliers start: 29
  outliers final: 19
  residues processed: 134
  average time/residue: 0.1941
  time to fit residues: 37.7737
Evaluate side-chains
  129 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 319 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.197495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.147615 restraints weight = 10065.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.147488 restraints weight = 10322.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.149482 restraints weight = 8731.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7964  Z= 0.171
  Angle     :  0.591  10.886  10779  Z= 0.305
  Chirality :  0.041   0.168   1160
  Planarity :  0.003   0.042   1384
  Dihedral  :  4.160  21.063   1060
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.05 %
    Favored  : 75.51 %
  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:  0.26 (0.28), residues: 940
  helix:  1.54 (0.24), residues: 503
  sheet: -1.09 (0.58), residues: 79
  loop : -1.55 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  45 
 HIS   0.004   0.001   HIS A 143 
 PHE   0.010   0.001   PHE A 452 
 TYR   0.013   0.001   TYR A 619 
 ARG   0.003   0.000   ARG B 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03750 (  405)
  hydrogen bonds       : angle       4.30567 ( 1206)
  SS BOND              : bond        0.00185 (    4)
  SS BOND              : angle       0.91521 (    8)
  covalent geometry    : bond        0.00394 ( 7960)
  covalent geometry    : angle       0.59100 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8922 (ttm) cc_final: 0.8560 (mtp)
REVERT: A  183 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8088 (mm-40)
REVERT: A  237 TRP cc_start: 0.8581 (OUTLIER) cc_final: 0.8250 (t60)
REVERT: A  347 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8442 (mm)
REVERT: A  348 GLU cc_start: 0.7698 (tp30) cc_final: 0.7376 (tp30)
REVERT: A  380 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.7983 (m-10)
REVERT: A  428 ASN cc_start: 0.7167 (m110) cc_final: 0.6667 (t0)
REVERT: A  429 ASN cc_start: 0.6788 (t0) cc_final: 0.6566 (t0)
REVERT: A  444 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7846 (tp40)
REVERT: A  478 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9259 (mm)
REVERT: A  611 ASN cc_start: 0.7521 (t0) cc_final: 0.7208 (m-40)
REVERT: A  639 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8276 (tt0)
REVERT: A  666 TYR cc_start: 0.8281 (t80) cc_final: 0.7842 (t80)
REVERT: B   64 MET cc_start: 0.9027 (mmt) cc_final: 0.8743 (mmp)
REVERT: B  203 GLU cc_start: 0.2922 (OUTLIER) cc_final: 0.2670 (tm-30)
REVERT: B  216 SER cc_start: 0.2416 (OUTLIER) cc_final: 0.1455 (t)
  outliers start: 29
  outliers final: 19
  residues processed: 137
  average time/residue: 0.2256
  time to fit residues: 46.2401
Evaluate side-chains
  136 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  237 TRP
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0870
   chunk 54 optimal weight:    0.4980
   chunk 53 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
B  73 GLN
B 319 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.200832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.152072 restraints weight = 9854.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.150991 restraints weight = 10389.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.152493 restraints weight = 9778.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7964  Z= 0.124
  Angle     :  0.563  10.403  10779  Z= 0.288
  Chirality :  0.039   0.146   1160
  Planarity :  0.003   0.044   1384
  Dihedral  :  4.035  19.812   1060
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.05 %
    Favored  : 75.86 %
  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:  0.31 (0.28), residues: 940
  helix:  1.59 (0.24), residues: 504
  sheet: -1.05 (0.58), residues: 79
  loop : -1.56 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.009   0.001   PHE B  71 
 TYR   0.015   0.001   TYR A 619 
 ARG   0.003   0.000   ARG B 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03409 (  405)
  hydrogen bonds       : angle       4.18985 ( 1206)
  SS BOND              : bond        0.00171 (    4)
  SS BOND              : angle       0.77207 (    8)
  covalent geometry    : bond        0.00278 ( 7960)
  covalent geometry    : angle       0.56327 (10771)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.8427 (m-30) cc_final: 0.8199 (m-30)
REVERT: A  152 MET cc_start: 0.8867 (ttm) cc_final: 0.8505 (mtp)
REVERT: A  183 GLN cc_start: 0.8263 (mm-40) cc_final: 0.8016 (mm-40)
REVERT: A  347 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8427 (mm)
REVERT: A  348 GLU cc_start: 0.7808 (tp30) cc_final: 0.7447 (tp30)
REVERT: A  380 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.7902 (m-10)
REVERT: A  428 ASN cc_start: 0.7153 (m110) cc_final: 0.6658 (t0)
REVERT: A  429 ASN cc_start: 0.6731 (t0) cc_final: 0.6446 (t0)
REVERT: A  444 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7813 (tp40)
REVERT: A  478 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9210 (mm)
REVERT: A  517 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: A  611 ASN cc_start: 0.7457 (t0) cc_final: 0.7156 (m-40)
REVERT: A  639 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8215 (tt0)
REVERT: B   64 MET cc_start: 0.8993 (mmt) cc_final: 0.8690 (mmp)
REVERT: B  203 GLU cc_start: 0.2944 (OUTLIER) cc_final: 0.2702 (tm-30)
REVERT: B  216 SER cc_start: 0.2351 (OUTLIER) cc_final: 0.1387 (t)
REVERT: B  309 ASN cc_start: 0.7507 (p0) cc_final: 0.7086 (p0)
  outliers start: 26
  outliers final: 18
  residues processed: 134
  average time/residue: 0.1730
  time to fit residues: 33.3998
Evaluate side-chains
  131 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 319 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.196768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.147361 restraints weight = 9915.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.145424 restraints weight = 10591.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.147865 restraints weight = 9461.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7964  Z= 0.122
  Angle     :  0.574   9.841  10779  Z= 0.293
  Chirality :  0.039   0.138   1160
  Planarity :  0.003   0.051   1384
  Dihedral  :  3.979  19.821   1060
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.28 %
    Favored  : 75.51 %
  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:  0.35 (0.28), residues: 940
  helix:  1.63 (0.24), residues: 504
  sheet: -0.83 (0.57), residues: 82
  loop : -1.60 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 122 
 PHE   0.009   0.001   PHE B  71 
 TYR   0.014   0.001   TYR A 619 
 ARG   0.003   0.000   ARG B 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03368 (  405)
  hydrogen bonds       : angle       4.17269 ( 1206)
  SS BOND              : bond        0.00169 (    4)
  SS BOND              : angle       0.77983 (    8)
  covalent geometry    : bond        0.00274 ( 7960)
  covalent geometry    : angle       0.57412 (10771)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2854.61 seconds
wall clock time: 52 minutes 46.71 seconds (3166.71 seconds total)