Starting phenix.real_space_refine
on Fri Feb 14 20:03:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pmh_13533/02_2025/7pmh_13533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pmh_13533/02_2025/7pmh_13533.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pmh_13533/02_2025/7pmh_13533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pmh_13533/02_2025/7pmh_13533.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pmh_13533/02_2025/7pmh_13533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pmh_13533/02_2025/7pmh_13533.cif"
  }
  resolution = 3.4
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      3      5.21       5
     S      63      5.16       5
     C    6461      2.51       5
     N    1724      2.21       5
     O    1898      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10154
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 1059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1059
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 6070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 742, 6070
          Classifications: {'peptide': 742}
          Link IDs: {'PTRANS': 26, 'TRANS': 715}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2909
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 26
          Classifications: {'peptide': 4}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ANP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.40, per 1000 atoms: 0.63
  Number of scatterers: 10154
  At special positions: 0
  Unit cell: (102.3, 128.7, 157.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      63     16.00
     P       5     15.00
     Mg      3     11.99
     O    1898      8.00
     N    1724      7.00
     C    6461      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " TRP H   1 " - " ALA H   7 "
      " DTH H   4 " - " ALA H   3 "
  Time building additional restraints: 2.53
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DTH H   4 "
  Number of C-beta restraints generated:  2374

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 15 sheets defined
      55.0% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 19
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 4.287A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ASP B  34 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 52
    Processing helix  chain 'B' and resid 56 through 63
    Processing helix  chain 'B' and resid 67 through 79
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 87 through 95
    Processing helix  chain 'B' and resid 106 through 116
    Processing helix  chain 'B' and resid 121 through 130
    Processing helix  chain 'B' and resid 141 through 150
    Processing helix  chain 'A' and resid 81 through 95
    Processing helix  chain 'A' and resid 116 through 119
      removed outlier: 4.497A  pdb=" N   TYR A 119 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 116 through 119'
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 131 through 135
    Processing helix  chain 'A' and resid 138 through 154
      removed outlier: 3.783A  pdb=" N   GLN A 149 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 184
      removed outlier: 3.733A  pdb=" N   PHE A 180 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 198
    Processing helix  chain 'A' and resid 199 through 207
    Processing helix  chain 'A' and resid 245 through 250
    Processing helix  chain 'A' and resid 259 through 268
      removed outlier: 4.163A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 271
      No H-bonds generated for 'chain 'A' and resid 269 through 271'
    Processing helix  chain 'A' and resid 273 through 278
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 3.864A  pdb=" N   GLN A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 315
      removed outlier: 3.712A  pdb=" N   GLU A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 336
      removed outlier: 3.624A  pdb=" N   MET A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 367 through 375
    Processing helix  chain 'A' and resid 392 through 424
    Processing helix  chain 'A' and resid 448 through 481
    Processing helix  chain 'A' and resid 483 through 487
      removed outlier: 3.766A  pdb=" N   LEU A 486 " --> pdb=" O   PRO A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 500
    Processing helix  chain 'A' and resid 504 through 515
      removed outlier: 3.821A  pdb=" N   LYS A 514 " --> pdb=" O   ASP A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 532
      removed outlier: 3.525A  pdb=" N   GLN A 525 " --> pdb=" O   ASP A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 569
      removed outlier: 3.607A  pdb=" N   LYS A 567 " --> pdb=" O   GLY A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 582
      removed outlier: 3.607A  pdb=" N   ILE A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 4.034A  pdb=" N   PHE A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLN A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 635 through 654
      removed outlier: 3.905A  pdb=" N   ALA A 653 " --> pdb=" O   GLU A 649 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   THR A 654 " --> pdb=" O   THR A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 685
      removed outlier: 3.612A  pdb=" N   VAL A 679 " --> pdb=" O   GLU A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 696
    Processing helix  chain 'A' and resid 704 through 712
    Processing helix  chain 'A' and resid 723 through 736
    Processing helix  chain 'A' and resid 754 through 792
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 79 through 93
      removed outlier: 3.577A  pdb=" N   ILE C  85 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 4.067A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
      removed outlier: 3.667A  pdb=" N   SER C 141 " --> pdb=" O   GLN C 137 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   TYR C 143 " --> pdb=" O   VAL C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 175
      removed outlier: 3.747A  pdb=" N   ILE C 175 " --> pdb=" O   PRO C 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 172 through 175'
    Processing helix  chain 'C' and resid 182 through 196
      removed outlier: 3.777A  pdb=" N   THR C 186 " --> pdb=" O   GLY C 182 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LYS C 191 " --> pdb=" O   ASP C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.529A  pdb=" N   GLU C 207 " --> pdb=" O   THR C 203 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
    Processing helix  chain 'C' and resid 252 through 257
    Processing helix  chain 'C' and resid 258 through 262
    Processing helix  chain 'C' and resid 273 through 283
    Processing helix  chain 'C' and resid 289 through 294
    Processing helix  chain 'C' and resid 301 through 305
    Processing helix  chain 'C' and resid 308 through 321
    Processing helix  chain 'C' and resid 334 through 336
      No H-bonds generated for 'chain 'C' and resid 334 through 336'
    Processing helix  chain 'C' and resid 337 through 348
      removed outlier: 3.682A  pdb=" N   SER C 348 " --> pdb=" O   SER C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 355
      removed outlier: 3.971A  pdb=" N   PHE C 352 " --> pdb=" O   LEU C 349 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN C 354 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 368 through 374
      removed outlier: 4.104A  pdb=" N   ARG C 372 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28
    Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105
    Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 16
      removed outlier: 7.066A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A  48 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 103
      removed outlier: 6.439A  pdb=" N   SER A 158 " --> pdb=" O   HIS A 657 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   VAL A 659 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   CYS A 661 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   SER A 162 " --> pdb=" O   CYS A 661 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLN A 157 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   LEU A 436 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ILE A 159 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   ILE A 438 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   VAL A 161 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLY A 236 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 211
      removed outlier: 5.392A  pdb=" N   ALA A 209 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342
    Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 382
    Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703
      removed outlier: 3.671A  pdb=" N   SER A 700 " --> pdb=" O   PHE A 751 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.691A  pdb=" N   THR C 106 " --> pdb=" O   CYS C  10 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   THR C 103 " --> pdb=" O   TYR C 133 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   ALA C 135 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU C 105 " --> pdb=" O   ALA C 135 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170
      removed outlier: 6.092A  pdb=" N   ASN C 297 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241

    521 hydrogen bonds defined for protein.
    1455 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: 3.51

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1694
        1.31 -     1.44: 2739
        1.44 -     1.56: 5823
        1.56 -     1.69: 8
        1.69 -     1.81: 103
  Bond restraints: 10367
  Sorted by residual:
  bond pdb=" O3A ANP A1901 "
       pdb=" PB  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.700  1.551  0.149 2.00e-02 2.50e+03 5.53e+01
  bond pdb=" CA  EEP H   2 "
       pdb=" C   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.572  1.439  0.133 2.00e-02 2.50e+03 4.39e+01
  bond pdb=" N3B ANP A1901 "
       pdb=" PG  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.795  1.690  0.105 2.00e-02 2.50e+03 2.75e+01
  bond pdb=" O5' ANP A1901 "
       pdb=" PA  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.655  1.571  0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" C   EEP H   2 "
       pdb=" O   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.263  1.196  0.067 2.00e-02 2.50e+03 1.11e+01
  ... (remaining 10362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 13806
        3.25 -     6.50: 175
        6.50 -     9.75: 18
        9.75 -    13.00: 5
       13.00 -    16.25: 1
  Bond angle restraints: 14005
  Sorted by residual:
  angle pdb=" C   HYP H   6 "
        pdb=" N   ALA H   7 "
        pdb=" CA  ALA H   7 "
      ideal   model   delta    sigma   weight residual
     121.70  110.78   10.92 1.80e+00 3.09e-01 3.68e+01
  angle pdb=" N   DTH H   4 "
        pdb=" CA  DTH H   4 "
        pdb=" CB  DTH H   4 "
      ideal   model   delta    sigma   weight residual
     111.50  101.96    9.54 1.70e+00 3.46e-01 3.15e+01
  angle pdb=" PB  ANP A1901 "
        pdb=" N3B ANP A1901 "
        pdb=" PG  ANP A1901 "
      ideal   model   delta    sigma   weight residual
     126.95  110.70   16.25 3.00e+00 1.11e-01 2.94e+01
  angle pdb=" C   TRP H   1 "
        pdb=" CA  TRP H   1 "
        pdb=" CB  TRP H   1 "
      ideal   model   delta    sigma   weight residual
     110.10   99.89   10.21 1.90e+00 2.77e-01 2.89e+01
  angle pdb=" N   GLY A 563 "
        pdb=" CA  GLY A 563 "
        pdb=" C   GLY A 563 "
      ideal   model   delta    sigma   weight residual
     113.86  121.71   -7.85 1.50e+00 4.44e-01 2.74e+01
  ... (remaining 14000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.34: 6003
       26.34 -    52.68: 211
       52.68 -    79.02: 42
       79.02 -   105.36: 16
      105.36 -   131.70: 3
  Dihedral angle restraints: 6275
    sinusoidal: 2594
      harmonic: 3681
  Sorted by residual:
  dihedral pdb=" C5' ADP C 401 "
           pdb=" O5' ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" O2A ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  168.30  131.70     1      2.00e+01 2.50e-03 4.00e+01
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   67.81 -127.82     1      2.00e+01 2.50e-03 3.87e+01
  dihedral pdb=" O2A ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" PB  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   64.63 -124.63     1      2.00e+01 2.50e-03 3.76e+01
  ... (remaining 6272 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1000
       0.052 -    0.105: 415
       0.105 -    0.157: 99
       0.157 -    0.209: 13
       0.209 -    0.261: 3
  Chirality restraints: 1530
  Sorted by residual:
  chirality pdb=" C3' ANP A1901 "
            pdb=" C2' ANP A1901 "
            pdb=" C4' ANP A1901 "
            pdb=" O3' ANP A1901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.62    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  GLU C 316 "
            pdb=" N   GLU C 316 "
            pdb=" C   GLU C 316 "
            pdb=" CB  GLU C 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  GLU C 226 "
            pdb=" N   GLU C 226 "
            pdb=" C   GLU C 226 "
            pdb=" CB  GLU C 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1527 not shown)

  Planarity restraints: 1787
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 306 "   -0.006 2.00e-02 2.50e+03   3.77e-02 2.85e+01
        pdb=" CG  TYR C 306 "    0.002 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 306 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 306 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 306 "    0.053 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 306 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 306 "    0.053 2.00e-02 2.50e+03
        pdb=" OH  TYR C 306 "   -0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 147 "   -0.129 9.50e-02 1.11e+02   7.14e-02 2.41e+01
        pdb=" NE  ARG C 147 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 147 "   -0.080 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 147 "    0.028 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 147 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 564 "   -0.040 2.00e-02 2.50e+03   3.64e-02 2.32e+01
        pdb=" CG  PHE A 564 "    0.084 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 564 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 564 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 564 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 564 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 564 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1784 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.37: 19
        2.37 -     3.00: 5576
        3.00 -     3.63: 14852
        3.63 -     4.27: 22558
        4.27 -     4.90: 38587
  Nonbonded interactions: 81592
  Sorted by model distance:
  nonbonded pdb=" CD1 TRP H   1 "
            pdb=" SG  CYS H   5 "
     model   vdw
     1.732 3.620
  nonbonded pdb=" O3G ANP A1901 "
            pdb="MG    MG A1902 "
     model   vdw
     2.000 2.170
  nonbonded pdb=" O1A ANP A1901 "
            pdb="MG    MG A1903 "
     model   vdw
     2.020 2.170
  nonbonded pdb=" O3B ADP C 401 "
            pdb="MG    MG C 402 "
     model   vdw
     2.024 2.170
  nonbonded pdb=" O1B ANP A1901 "
            pdb="MG    MG A1903 "
     model   vdw
     2.038 2.170
  ... (remaining 81587 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.850
  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:             0.000
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.470
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
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      :  0.009   0.149  10367  Z= 0.607
  Angle     :  1.005  16.253  14005  Z= 0.575
  Chirality :  0.058   0.261   1530
  Planarity :  0.008   0.089   1785
  Dihedral  : 15.498 131.704   3895
  Min Nonbonded Distance : 1.732

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.19 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.20), residues: 1230
  helix: -1.62 (0.17), residues: 599
  sheet:  0.02 (0.36), residues: 166
  loop : -0.16 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.005   TRP C 356 
 HIS   0.017   0.003   HIS C 275 
 PHE   0.084   0.003   PHE A 564 
 TYR   0.058   0.007   TYR C 306 
 ARG   0.081   0.011   ARG C 147 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.8764 (m-80) cc_final: 0.8459 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 92
  average time/residue: 0.2978
  time to fit residues: 36.9109
Evaluate side-chains
  55 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.8980
   chunk 93 optimal weight:    0.7980
   chunk 52 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 112 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
A  72 ASN
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 ASN
A 264 GLN
A 290 GLN
A 410 ASN
A 775 GLN
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 137 GLN
** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 162 ASN
C 371 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.048678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.035030 restraints weight = 57216.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.2774 rms_B_bonded: 4.01
r_work: 0.2613 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10367  Z= 0.189
  Angle     :  0.614   7.241  14005  Z= 0.326
  Chirality :  0.043   0.210   1530
  Planarity :  0.004   0.050   1785
  Dihedral  : 10.385 144.084   1424
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  3.52 %
    Favored  : 95.56 %
  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:  0.84 (0.23), residues: 1230
  helix:  0.82 (0.21), residues: 618
  sheet:  0.58 (0.36), residues: 174
  loop :  0.40 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 484 
 HIS   0.007   0.001   HIS C 275 
 PHE   0.018   0.001   PHE A 564 
 TYR   0.021   0.001   TYR A  10 
 ARG   0.005   0.001   ARG C  95 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9431 (m-80) cc_final: 0.8788 (m-10)
REVERT: A  177 MET cc_start: 0.9511 (ttm) cc_final: 0.9156 (tmm)
REVERT: A  478 MET cc_start: 0.8865 (mmp) cc_final: 0.8135 (mmp)
REVERT: A  783 MET cc_start: 0.9347 (tpt) cc_final: 0.9140 (tpp)
REVERT: C  190 MET cc_start: 0.8858 (mtp) cc_final: 0.8496 (mtt)
REVERT: C  195 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8446 (mt-10)
REVERT: C  205 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8575 (mt-10)
REVERT: C  227 MET cc_start: 0.8764 (tpp) cc_final: 0.8451 (tpp)
REVERT: C  313 MET cc_start: 0.9641 (tpp) cc_final: 0.9406 (mmt)
  outliers start: 10
  outliers final: 2
  residues processed: 68
  average time/residue: 0.2483
  time to fit residues: 24.9821
Evaluate side-chains
  62 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 45 optimal weight:    0.0000
   chunk 71 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0870
   chunk 42 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.5362

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.048765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.035215 restraints weight = 57835.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 4.01
r_work: 0.2625 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10367  Z= 0.151
  Angle     :  0.549   7.680  14005  Z= 0.285
  Chirality :  0.041   0.163   1530
  Planarity :  0.004   0.050   1785
  Dihedral  :  9.696 149.419   1423
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  5.09 %
    Favored  : 94.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.24), residues: 1230
  helix:  1.43 (0.21), residues: 620
  sheet:  0.79 (0.37), residues: 180
  loop :  0.43 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 484 
 HIS   0.005   0.001   HIS C 275 
 PHE   0.012   0.001   PHE C 255 
 TYR   0.014   0.001   TYR A  10 
 ARG   0.003   0.000   ARG B  21 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9419 (m-80) cc_final: 0.8779 (m-10)
REVERT: A  132 MET cc_start: 0.7342 (mmt) cc_final: 0.7034 (mmp)
REVERT: A  135 MET cc_start: 0.8799 (ttp) cc_final: 0.8535 (ttt)
REVERT: A  478 MET cc_start: 0.9050 (mmp) cc_final: 0.8831 (mmp)
REVERT: A  783 MET cc_start: 0.9385 (tpt) cc_final: 0.9129 (tpp)
REVERT: C  190 MET cc_start: 0.8902 (mtp) cc_final: 0.8556 (mtt)
REVERT: C  205 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8582 (mt-10)
REVERT: C  227 MET cc_start: 0.8802 (tpp) cc_final: 0.8521 (tpp)
REVERT: C  283 MET cc_start: 0.9188 (mmm) cc_final: 0.8849 (mmm)
REVERT: C  313 MET cc_start: 0.9607 (tpp) cc_final: 0.9405 (mmt)
  outliers start: 4
  outliers final: 3
  residues processed: 65
  average time/residue: 0.2556
  time to fit residues: 24.3959
Evaluate side-chains
  57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 121 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 GLN
** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.048198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.034604 restraints weight = 57959.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.2762 rms_B_bonded: 3.99
r_work: 0.2605 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10367  Z= 0.199
  Angle     :  0.531   9.361  14005  Z= 0.274
  Chirality :  0.041   0.168   1530
  Planarity :  0.004   0.050   1785
  Dihedral  :  9.421 155.063   1423
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  6.66 %
    Favored  : 92.88 %
  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:  1.57 (0.24), residues: 1230
  helix:  1.62 (0.21), residues: 631
  sheet:  0.96 (0.39), residues: 165
  loop :  0.34 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 484 
 HIS   0.005   0.001   HIS C 275 
 PHE   0.013   0.001   PHE C 255 
 TYR   0.012   0.001   TYR A  10 
 ARG   0.002   0.000   ARG A 784 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 1.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9411 (m-80) cc_final: 0.8795 (m-10)
REVERT: A  132 MET cc_start: 0.7043 (mmt) cc_final: 0.6716 (mmp)
REVERT: A  135 MET cc_start: 0.8766 (ttp) cc_final: 0.8526 (ttp)
REVERT: A  305 MET cc_start: 0.9470 (tpp) cc_final: 0.9139 (tpp)
REVERT: A  478 MET cc_start: 0.9086 (mmp) cc_final: 0.7833 (mmp)
REVERT: C  190 MET cc_start: 0.8966 (mtp) cc_final: 0.8620 (mtt)
REVERT: C  205 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8604 (mt-10)
REVERT: C  227 MET cc_start: 0.8844 (tpp) cc_final: 0.8326 (tmm)
REVERT: C  283 MET cc_start: 0.9167 (mmm) cc_final: 0.8943 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 59
  average time/residue: 0.2376
  time to fit residues: 21.0315
Evaluate side-chains
  54 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 111 optimal weight:    0.8980
   chunk 114 optimal weight:    0.6980
   chunk 18 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.047737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.034155 restraints weight = 57676.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 4.00
r_work: 0.2593 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10367  Z= 0.221
  Angle     :  0.532   7.460  14005  Z= 0.274
  Chirality :  0.041   0.166   1530
  Planarity :  0.004   0.049   1785
  Dihedral  :  9.330 165.376   1423
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  7.22 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.24), residues: 1230
  helix:  1.78 (0.21), residues: 625
  sheet:  1.09 (0.39), residues: 169
  loop :  0.27 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP A 484 
 HIS   0.004   0.001   HIS A  81 
 PHE   0.013   0.001   PHE C 255 
 TYR   0.012   0.001   TYR A  10 
 ARG   0.003   0.000   ARG A 789 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 1.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9431 (m-80) cc_final: 0.8835 (m-10)
REVERT: A  132 MET cc_start: 0.6907 (mmt) cc_final: 0.6542 (mmp)
REVERT: A  177 MET cc_start: 0.9496 (ptm) cc_final: 0.9182 (ppp)
REVERT: A  305 MET cc_start: 0.9479 (tpp) cc_final: 0.9109 (tpp)
REVERT: A  478 MET cc_start: 0.9271 (mmp) cc_final: 0.8169 (mmp)
REVERT: C  190 MET cc_start: 0.9003 (mtp) cc_final: 0.8670 (mtt)
REVERT: C  227 MET cc_start: 0.8882 (tpp) cc_final: 0.8391 (tmm)
  outliers start: 8
  outliers final: 4
  residues processed: 60
  average time/residue: 0.2334
  time to fit residues: 20.9589
Evaluate side-chains
  53 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 109 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9980
   chunk 45 optimal weight:    0.1980
   chunk 54 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 114 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.048287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.034742 restraints weight = 57905.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 4.01
r_work: 0.2616 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10367  Z= 0.152
  Angle     :  0.515   9.508  14005  Z= 0.263
  Chirality :  0.040   0.163   1530
  Planarity :  0.003   0.046   1785
  Dihedral  :  9.171 175.332   1423
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  7.96 %
    Favored  : 91.49 %
  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:  1.81 (0.24), residues: 1230
  helix:  1.91 (0.21), residues: 619
  sheet:  1.15 (0.39), residues: 169
  loop :  0.30 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP A 484 
 HIS   0.004   0.001   HIS A  81 
 PHE   0.011   0.001   PHE C 255 
 TYR   0.008   0.001   TYR A  10 
 ARG   0.002   0.000   ARG A 677 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9420 (m-80) cc_final: 0.8825 (m-10)
REVERT: A  132 MET cc_start: 0.7006 (mmt) cc_final: 0.6719 (mmp)
REVERT: A  177 MET cc_start: 0.9435 (ptm) cc_final: 0.9094 (ppp)
REVERT: A  305 MET cc_start: 0.9515 (tpp) cc_final: 0.9087 (tpp)
REVERT: A  418 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8658 (m-70)
REVERT: A  478 MET cc_start: 0.9399 (mmp) cc_final: 0.9085 (mmm)
REVERT: C  190 MET cc_start: 0.8991 (mtp) cc_final: 0.8653 (mtt)
REVERT: C  205 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8640 (mt-10)
REVERT: C  227 MET cc_start: 0.8874 (tpp) cc_final: 0.8397 (tmm)
REVERT: C  283 MET cc_start: 0.9135 (mmm) cc_final: 0.8790 (mmm)
REVERT: C  311 ASP cc_start: 0.9136 (t0) cc_final: 0.8905 (t0)
REVERT: C  325 MET cc_start: 0.8684 (ptp) cc_final: 0.8316 (ptt)
  outliers start: 6
  outliers final: 3
  residues processed: 63
  average time/residue: 0.2282
  time to fit residues: 21.2486
Evaluate side-chains
  57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 102 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 55 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.048032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.034328 restraints weight = 58832.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.2758 rms_B_bonded: 4.05
r_work: 0.2599 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10367  Z= 0.193
  Angle     :  0.542   9.929  14005  Z= 0.275
  Chirality :  0.041   0.165   1530
  Planarity :  0.003   0.045   1785
  Dihedral  :  8.656 148.193   1423
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.33 %
    Favored  : 91.12 %
  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:  1.82 (0.24), residues: 1230
  helix:  1.97 (0.21), residues: 614
  sheet:  1.19 (0.42), residues: 160
  loop :  0.25 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 484 
 HIS   0.004   0.001   HIS A  81 
 PHE   0.012   0.001   PHE C 255 
 TYR   0.009   0.001   TYR A 259 
 ARG   0.002   0.000   ARG A 701 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8739 (ptpp)
REVERT: B   93 PHE cc_start: 0.9430 (m-80) cc_final: 0.8851 (m-10)
REVERT: B  120 MET cc_start: 0.7951 (mmt) cc_final: 0.6690 (mmm)
REVERT: A  177 MET cc_start: 0.9421 (ptm) cc_final: 0.9078 (ppp)
REVERT: A  305 MET cc_start: 0.9526 (tpp) cc_final: 0.9095 (tpp)
REVERT: C  190 MET cc_start: 0.9010 (mtp) cc_final: 0.8671 (mtt)
REVERT: C  205 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8628 (mt-10)
REVERT: C  227 MET cc_start: 0.8889 (tpp) cc_final: 0.8413 (tmm)
REVERT: C  283 MET cc_start: 0.9138 (mmm) cc_final: 0.8850 (mmm)
REVERT: C  311 ASP cc_start: 0.9143 (t0) cc_final: 0.8899 (t0)
REVERT: C  325 MET cc_start: 0.8737 (ptp) cc_final: 0.8332 (ptt)
  outliers start: 6
  outliers final: 4
  residues processed: 57
  average time/residue: 0.2313
  time to fit residues: 19.6753
Evaluate side-chains
  57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9980
   chunk 81 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0170
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.048492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.034960 restraints weight = 57781.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.2783 rms_B_bonded: 4.00
r_work: 0.2624 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10367  Z= 0.150
  Angle     :  0.528   9.598  14005  Z= 0.266
  Chirality :  0.040   0.174   1530
  Planarity :  0.003   0.049   1785
  Dihedral  :  8.016 113.447   1423
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  9.07 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.25), residues: 1230
  helix:  2.07 (0.22), residues: 612
  sheet:  1.21 (0.42), residues: 160
  loop :  0.32 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 484 
 HIS   0.005   0.001   HIS A  81 
 PHE   0.009   0.001   PHE C 255 
 TYR   0.008   0.001   TYR A 456 
 ARG   0.003   0.000   ARG A 701 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.9089 (tpp) cc_final: 0.8847 (tpp)
REVERT: B   61 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8722 (ptpp)
REVERT: B   93 PHE cc_start: 0.9430 (m-80) cc_final: 0.8848 (m-10)
REVERT: B  120 MET cc_start: 0.8025 (mmt) cc_final: 0.6987 (mmm)
REVERT: A  177 MET cc_start: 0.9412 (ptm) cc_final: 0.9045 (ppp)
REVERT: A  305 MET cc_start: 0.9515 (tpp) cc_final: 0.9158 (tpp)
REVERT: A  418 HIS cc_start: 0.9024 (OUTLIER) cc_final: 0.8659 (m-70)
REVERT: A  788 MET cc_start: 0.9254 (pmm) cc_final: 0.9032 (pmm)
REVERT: C  190 MET cc_start: 0.9000 (mtp) cc_final: 0.8664 (mtt)
REVERT: C  205 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8636 (mt-10)
REVERT: C  227 MET cc_start: 0.8889 (tpp) cc_final: 0.8427 (tmm)
REVERT: C  283 MET cc_start: 0.9130 (mmm) cc_final: 0.8711 (mpp)
REVERT: C  311 ASP cc_start: 0.9158 (t0) cc_final: 0.8922 (t0)
REVERT: C  325 MET cc_start: 0.8652 (ptp) cc_final: 0.8284 (ptt)
  outliers start: 6
  outliers final: 3
  residues processed: 60
  average time/residue: 0.2240
  time to fit residues: 20.3442
Evaluate side-chains
  56 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 65 optimal weight:    0.2980
   chunk 82 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.048472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.034930 restraints weight = 57970.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.2780 rms_B_bonded: 4.02
r_work: 0.2622 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10367  Z= 0.159
  Angle     :  0.532   9.252  14005  Z= 0.267
  Chirality :  0.040   0.164   1530
  Planarity :  0.003   0.050   1785
  Dihedral  :  7.977 111.575   1423
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  9.25 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.25), residues: 1230
  helix:  2.13 (0.22), residues: 607
  sheet:  1.25 (0.42), residues: 160
  loop :  0.33 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 484 
 HIS   0.005   0.001   HIS A  81 
 PHE   0.010   0.001   PHE C 255 
 TYR   0.008   0.001   TYR A  10 
 ARG   0.002   0.000   ARG A 701 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.9130 (tpp) cc_final: 0.8911 (tpp)
REVERT: B   61 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8715 (ptpp)
REVERT: B   93 PHE cc_start: 0.9425 (m-80) cc_final: 0.8817 (m-10)
REVERT: B  120 MET cc_start: 0.7979 (mmt) cc_final: 0.7048 (mmm)
REVERT: A  177 MET cc_start: 0.9419 (ptm) cc_final: 0.9052 (ppp)
REVERT: A  305 MET cc_start: 0.9521 (tpp) cc_final: 0.9146 (tpp)
REVERT: A  418 HIS cc_start: 0.9021 (OUTLIER) cc_final: 0.8651 (m-70)
REVERT: C  190 MET cc_start: 0.9004 (mtp) cc_final: 0.8671 (mtt)
REVERT: C  205 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8649 (mt-10)
REVERT: C  227 MET cc_start: 0.8884 (tpp) cc_final: 0.8416 (tmm)
REVERT: C  283 MET cc_start: 0.9133 (mmm) cc_final: 0.8764 (mpp)
REVERT: C  311 ASP cc_start: 0.9163 (t0) cc_final: 0.8926 (t0)
REVERT: C  325 MET cc_start: 0.8681 (ptp) cc_final: 0.8335 (ptt)
  outliers start: 5
  outliers final: 3
  residues processed: 58
  average time/residue: 0.2261
  time to fit residues: 19.9721
Evaluate side-chains
  57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0870
   chunk 17 optimal weight:    0.0470
   chunk 81 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0670
   overall best weight:    0.3194

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.049161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.035657 restraints weight = 57592.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 4.04
r_work: 0.2652 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10367  Z= 0.123
  Angle     :  0.517   9.286  14005  Z= 0.260
  Chirality :  0.039   0.163   1530
  Planarity :  0.003   0.051   1785
  Dihedral  :  7.742 100.765   1423
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  9.44 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.25), residues: 1230
  helix:  2.17 (0.22), residues: 607
  sheet:  1.26 (0.42), residues: 160
  loop :  0.32 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 484 
 HIS   0.006   0.001   HIS A  81 
 PHE   0.009   0.001   PHE C 255 
 TYR   0.008   0.001   TYR C  91 
 ARG   0.002   0.000   ARG A 701 

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.9125 (tpp) cc_final: 0.8907 (tpp)
REVERT: B   93 PHE cc_start: 0.9475 (m-80) cc_final: 0.8871 (m-10)
REVERT: B  120 MET cc_start: 0.7974 (mmt) cc_final: 0.7097 (mmm)
REVERT: A  177 MET cc_start: 0.9428 (ptm) cc_final: 0.9074 (ppp)
REVERT: A  305 MET cc_start: 0.9526 (tpp) cc_final: 0.9143 (tpp)
REVERT: A  371 MET cc_start: 0.9444 (mmm) cc_final: 0.9225 (tpp)
REVERT: A  418 HIS cc_start: 0.9035 (OUTLIER) cc_final: 0.8651 (m-70)
REVERT: A  759 LEU cc_start: 0.9693 (mp) cc_final: 0.9408 (tp)
REVERT: C  190 MET cc_start: 0.8988 (mtp) cc_final: 0.8656 (mtt)
REVERT: C  205 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8678 (mt-10)
REVERT: C  227 MET cc_start: 0.8874 (tpp) cc_final: 0.8421 (tmm)
REVERT: C  311 ASP cc_start: 0.9146 (t0) cc_final: 0.8910 (t0)
REVERT: C  325 MET cc_start: 0.8677 (ptp) cc_final: 0.8350 (ptt)
  outliers start: 3
  outliers final: 1
  residues processed: 61
  average time/residue: 0.2255
  time to fit residues: 20.8380
Evaluate side-chains
  57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  549 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.048297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.034839 restraints weight = 57537.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 3.99
r_work: 0.2618 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10367  Z= 0.184
  Angle     :  0.553  12.978  14005  Z= 0.275
  Chirality :  0.040   0.166   1530
  Planarity :  0.004   0.051   1785
  Dihedral  :  7.786 102.117   1423
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  9.34 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.25), residues: 1230
  helix:  2.16 (0.22), residues: 607
  sheet:  1.34 (0.42), residues: 160
  loop :  0.33 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 484 
 HIS   0.004   0.001   HIS A  81 
 PHE   0.014   0.001   PHE B  12 
 TYR   0.009   0.001   TYR A  10 
 ARG   0.002   0.000   ARG A 701 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4647.28 seconds
wall clock time: 83 minutes 25.55 seconds (5005.55 seconds total)