Starting phenix.real_space_refine
on Tue Feb 11 10:58:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7etw_31303/02_2025/7etw_31303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7etw_31303/02_2025/7etw_31303.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7etw_31303/02_2025/7etw_31303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7etw_31303/02_2025/7etw_31303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7etw_31303/02_2025/7etw_31303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7etw_31303/02_2025/7etw_31303.cif"
  }
  resolution = 4.1
  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      20      5.16       5
     C    3204      2.51       5
     N     784      2.21       5
     O     944      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4952
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1525
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 8, 'TRANS': 188}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 3059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 483, 3059
          Classifications: {'peptide': 483}
          Incomplete info: {'truncation_to_alanine': 225}
          Link IDs: {'PTRANS': 25, 'TRANS': 457}
          Chain breaks: 3
          Unresolved chain link angles: 16
          Unresolved non-hydrogen bonds: 852
          Unresolved non-hydrogen angles: 1104
          Unresolved non-hydrogen dihedrals: 724
          Unresolved non-hydrogen chiralities: 83
          Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 6, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 13, 'ARG:plan': 18}
          Unresolved non-hydrogen planarities: 456
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 340
          Unusual residues: {'AJP': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 3.75, per 1000 atoms: 0.76
  Number of scatterers: 4952
  At special positions: 0
  Unit cell: (85.098, 86.189, 123.283, 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      20     16.00
     O     944      8.00
     N     784      7.00
     C    3204      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
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN B 641 "
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 734.7 milliseconds
  

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1274

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      64.3% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 48
    Processing helix  chain 'A' and resid 61 through 67
    Processing helix  chain 'A' and resid 72 through 95
      removed outlier: 4.008A  pdb=" N   CYS A  76 " --> pdb=" O   TRP A  72 " (cutoff:3.500A)
      Proline residue:  A  89  - end of helix
      removed outlier: 3.812A  pdb=" N   ASP A  92 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 121
      removed outlier: 3.791A  pdb=" N   VAL A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 147
      removed outlier: 3.525A  pdb=" N   LEU A 133 " --> pdb=" O   ASN A 129 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ALA A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 173
      removed outlier: 3.575A  pdb=" N   GLY A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 184
      No H-bonds generated for 'chain 'A' and resid 182 through 184'
    Processing helix  chain 'A' and resid 185 through 191
      removed outlier: 4.007A  pdb=" N   ARG A 189 " --> pdb=" O   PHE A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 212
      removed outlier: 3.584A  pdb=" N   ILE A 195 " --> pdb=" O   TRP A 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 23
      removed outlier: 3.605A  pdb=" N   PHE B  15 " --> pdb=" O   ILE B  11 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA B  23 " --> pdb=" O   GLY B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 41
      removed outlier: 3.811A  pdb=" N   ILE B  29 " --> pdb=" O   TYR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 131
      removed outlier: 3.626A  pdb=" N   SER B 117 " --> pdb=" O   ASP B 113 " (cutoff:3.500A)
      Proline residue:  B 118  - end of helix
      removed outlier: 3.951A  pdb=" N   GLN B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASN B 131 " --> pdb=" O   GLU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 146
      removed outlier: 3.501A  pdb=" N   GLU B 145 " --> pdb=" O   SER B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 161
      removed outlier: 3.705A  pdb=" N   ARG B 158 " --> pdb=" O   PRO B 155 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   LYS B 159 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 179
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 191 through 197
    Processing helix  chain 'B' and resid 209 through 215
    Processing helix  chain 'B' and resid 244 through 259
      removed outlier: 3.605A  pdb=" N   LEU B 248 " --> pdb=" O   HIS B 244 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   SER B 250 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU B 257 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 284
      No H-bonds generated for 'chain 'B' and resid 282 through 284'
    Processing helix  chain 'B' and resid 285 through 305
      removed outlier: 3.716A  pdb=" N   VAL B 289 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LYS B 305 " --> pdb=" O   PHE B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 336
      removed outlier: 4.364A  pdb=" N   ALA B 316 " --> pdb=" O   LYS B 312 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ALA B 319 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 356
      removed outlier: 3.598A  pdb=" N   LEU B 352 " --> pdb=" O   ILE B 348 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL B 353 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 370
      removed outlier: 5.421A  pdb=" N   LEU B 364 " --> pdb=" O   ASN B 360 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   SER B 367 " --> pdb=" O   VAL B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 409
      removed outlier: 3.854A  pdb=" N   ARG B 380 " --> pdb=" O   GLU B 376 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER B 386 " --> pdb=" O   ALA B 382 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER B 387 " --> pdb=" O   GLN B 383 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   TRP B 390 " --> pdb=" O   SER B 386 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   SER B 391 " --> pdb=" O   SER B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 433
      removed outlier: 4.607A  pdb=" N   LEU B 419 " --> pdb=" O   GLN B 415 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE B 420 " --> pdb=" O   GLU B 416 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   MET B 433 " --> pdb=" O   PHE B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 450
      removed outlier: 3.719A  pdb=" N   THR B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 533
    Processing helix  chain 'B' and resid 534 through 538
    Processing helix  chain 'B' and resid 632 through 639
      removed outlier: 3.996A  pdb=" N   LEU B 636 " --> pdb=" O   HIS B 632 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   PHE B 637 " --> pdb=" O   TRP B 633 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 171 through 172
      removed outlier: 3.805A  pdb=" N   VAL B 232 " --> pdb=" O   SER B 100 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL B  98 " --> pdb=" O   TYR B 234 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   VAL B 654 " --> pdb=" O   GLN B  95 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE B  97 " --> pdb=" O   VAL B 654 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 171 through 172
      removed outlier: 3.805A  pdb=" N   VAL B 232 " --> pdb=" O   SER B 100 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL B  98 " --> pdb=" O   TYR B 234 " (cutoff:3.500A)
      removed outlier: 8.364A  pdb=" N   THR B 658 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LYS B  99 " --> pdb=" O   THR B 658 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 136
      removed outlier: 3.882A  pdb=" N   LEU B 134 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 275
      removed outlier: 4.460A  pdb=" N   VAL B 272 " --> pdb=" O   LEU B 651 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU B 651 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)

    295 hydrogen bonds defined for protein.
    852 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 747
        1.32 -     1.44: 1388
        1.44 -     1.56: 2907
        1.56 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 5072
  Sorted by residual:
  bond pdb=" C   LYS B 277 "
       pdb=" O   LYS B 277 "
    ideal  model  delta    sigma   weight residual
    1.235  1.281 -0.047 1.18e-02 7.18e+03 1.57e+01
  bond pdb=" N   ARG B 660 "
       pdb=" CA  ARG B 660 "
    ideal  model  delta    sigma   weight residual
    1.458  1.504 -0.046 1.18e-02 7.18e+03 1.55e+01
  bond pdb=" N   VAL B 654 "
       pdb=" CA  VAL B 654 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.043 1.14e-02 7.69e+03 1.45e+01
  bond pdb=" N   VAL B 657 "
       pdb=" CA  VAL B 657 "
    ideal  model  delta    sigma   weight residual
    1.455  1.498 -0.043 1.18e-02 7.18e+03 1.32e+01
  bond pdb=" N   LYS B  99 "
       pdb=" CA  LYS B  99 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.045 1.24e-02 6.50e+03 1.30e+01
  ... (remaining 5067 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 6455
        2.09 -     4.18: 479
        4.18 -     6.27: 73
        6.27 -     8.36: 12
        8.36 -    10.45: 5
  Bond angle restraints: 7024
  Sorted by residual:
  angle pdb=" N   PRO B 104 "
        pdb=" CA  PRO B 104 "
        pdb=" C   PRO B 104 "
      ideal   model   delta    sigma   weight residual
     113.84  104.13    9.71 1.30e+00 5.92e-01 5.58e+01
  angle pdb=" N   ILE A  51 "
        pdb=" CA  ILE A  51 "
        pdb=" C   ILE A  51 "
      ideal   model   delta    sigma   weight residual
     106.32  116.68  -10.36 1.61e+00 3.86e-01 4.14e+01
  angle pdb=" CA  SER B 173 "
        pdb=" C   SER B 173 "
        pdb=" N   PRO B 174 "
      ideal   model   delta    sigma   weight residual
     117.95  122.09   -4.14 7.70e-01 1.69e+00 2.90e+01
  angle pdb=" C   ARG B 267 "
        pdb=" CA  ARG B 267 "
        pdb=" CB  ARG B 267 "
      ideal   model   delta    sigma   weight residual
     116.54  111.29    5.25 1.15e+00 7.56e-01 2.08e+01
  angle pdb=" C   PRO B  89 "
        pdb=" N   VAL B  90 "
        pdb=" CA  VAL B  90 "
      ideal   model   delta    sigma   weight residual
     122.48  128.15   -5.67 1.25e+00 6.40e-01 2.05e+01
  ... (remaining 7019 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.75: 3423
       22.75 -    45.51: 171
       45.51 -    68.26: 26
       68.26 -    91.02: 6
       91.02 -   113.77: 2
  Dihedral angle restraints: 3628
    sinusoidal: 1663
      harmonic: 1965
  Sorted by residual:
  dihedral pdb=" C   ILE A  51 "
           pdb=" N   ILE A  51 "
           pdb=" CA  ILE A  51 "
           pdb=" CB  ILE A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.18   11.18     0      2.50e+00 1.60e-01 2.00e+01
  dihedral pdb=" CA  LYS A 102 "
           pdb=" C   LYS A 102 "
           pdb=" N   ARG A 103 "
           pdb=" CA  ARG A 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.97  -22.03     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  VAL A  55 "
           pdb=" C   VAL A  55 "
           pdb=" N   THR A  56 "
           pdb=" CA  THR A  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.05  -19.95     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 3625 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.254: 958
       0.254 -    0.509: 5
       0.509 -    0.763: 0
       0.763 -    1.018: 0
       1.018 -    1.272: 1
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.13   -1.27 2.00e-02 2.50e+03 4.04e+03
  chirality pdb=" CA  ILE A  51 "
            pdb=" N   ILE A  51 "
            pdb=" C   ILE A  51 "
            pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.07    0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" C11 AJP A 302 "
            pdb=" C10 AJP A 302 "
            pdb=" C12 AJP A 302 "
            pdb=" C16 AJP A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.47   -0.27 2.00e-01 2.50e+01 1.81e+00
  ... (remaining 961 not shown)

  Planarity restraints: 813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.157 2.00e-02 2.50e+03   1.35e-01 2.27e+02
        pdb=" C7  NAG D   2 "    0.035 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.029 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.219 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.126 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 641 "    0.093 2.00e-02 2.50e+03   1.35e-01 2.26e+02
        pdb=" CG  ASN B 641 "   -0.041 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 641 "    0.039 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 641 "   -0.238 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "    0.148 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.113 2.00e-02 2.50e+03   9.24e-02 1.07e+02
        pdb=" C7  NAG D   1 "    0.030 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.084 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.147 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.020 2.00e-02 2.50e+03
  ... (remaining 810 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 29
        2.45 -     3.07: 4058
        3.07 -     3.68: 6953
        3.68 -     4.29: 9646
        4.29 -     4.90: 14668
  Nonbonded interactions: 35354
  Sorted by model distance:
  nonbonded pdb=" O53 AJP A 302 "
            pdb=" O76 AJP A 302 "
     model   vdw
     1.843 3.040
  nonbonded pdb=" O43 AJP A 304 "
            pdb=" O50 AJP A 304 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" O60 AJP A 303 "
            pdb=" O77 AJP A 303 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   ILE B 280 "
            pdb=" O   GLY B 281 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   ALA B 382 "
            pdb=" OG  SER B 386 "
     model   vdw
     2.268 3.040
  ... (remaining 35349 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.500
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
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   0.055   5072  Z= 0.617
  Angle     :  1.207  10.452   7024  Z= 0.682
  Chirality :  0.076   1.272    964
  Planarity :  0.008   0.135    812
  Dihedral  : 13.698 113.769   2354
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  1.94 %
    Allowed  : 11.64 %
    Favored  : 86.42 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  4.90 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.16 %
  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: -5.46 (0.24), residues: 670
  helix: -3.25 (0.19), residues: 375
  sheet: -1.07 (1.06), residues: 26
  loop : -4.37 (0.28), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 633 
 HIS   0.024   0.004   HIS B 632 
 PHE   0.013   0.002   PHE A 155 
 TYR   0.027   0.002   TYR A  88 
 ARG   0.005   0.001   ARG B 631 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 157
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ARG cc_start: 0.7952 (ttt90) cc_final: 0.6893 (tmt170)
REVERT: A  167 VAL cc_start: 0.9082 (t) cc_final: 0.8821 (p)
REVERT: A  208 ARG cc_start: 0.8669 (mtt180) cc_final: 0.7914 (mtt180)
REVERT: A  209 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7542 (tp-100)
REVERT: B  359 GLU cc_start: 0.7777 (mp0) cc_final: 0.7517 (mp0)
REVERT: B  378 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8018 (ttmm)
REVERT: B  383 GLN cc_start: 0.9147 (tt0) cc_final: 0.8482 (mt0)
REVERT: B  388 GLU cc_start: 0.8434 (tp30) cc_final: 0.7911 (tp30)
REVERT: B  442 ILE cc_start: 0.8824 (tp) cc_final: 0.8532 (mm)
REVERT: B  445 ARG cc_start: 0.8511 (ttt90) cc_final: 0.8018 (mmm160)
REVERT: B  447 MET cc_start: 0.7903 (ttt) cc_final: 0.7536 (ttm)
REVERT: B  626 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7315 (mmp80)
REVERT: B  627 LYS cc_start: 0.7899 (mttt) cc_final: 0.7563 (pttm)
REVERT: B  641 ASN cc_start: 0.6111 (t0) cc_final: 0.5609 (t0)
  outliers start: 5
  outliers final: 1
  residues processed: 160
  average time/residue: 0.1969
  time to fit residues: 38.4722
Evaluate side-chains
  106 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 50 optimal weight:    0.3980
   chunk 28 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:   50.0000
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 120 HIS
B  17 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.152764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.125764 restraints weight = 11627.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.129066 restraints weight = 6309.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.131335 restraints weight = 4361.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5072  Z= 0.274
  Angle     :  0.832   7.688   7024  Z= 0.397
  Chirality :  0.047   0.361    964
  Planarity :  0.006   0.088    812
  Dihedral  :  9.305  67.972   1629
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  6.72 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  8.45 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.30), residues: 670
  helix: -0.95 (0.24), residues: 391
  sheet: -1.33 (0.85), residues: 39
  loop : -3.30 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 146 
 HIS   0.011   0.002   HIS B 632 
 PHE   0.022   0.002   PHE B 301 
 TYR   0.023   0.002   TYR A  88 
 ARG   0.007   0.001   ARG A 103 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7196 (ptp-170)
REVERT: A  209 GLN cc_start: 0.8383 (tp-100) cc_final: 0.7750 (tp-100)
REVERT: B  298 TYR cc_start: 0.8679 (t80) cc_final: 0.8189 (t80)
REVERT: B  347 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7546 (mt-10)
REVERT: B  378 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8171 (ttmm)
REVERT: B  380 ARG cc_start: 0.8463 (ttt90) cc_final: 0.8182 (ttt180)
REVERT: B  383 GLN cc_start: 0.9091 (tt0) cc_final: 0.8585 (mt0)
REVERT: B  388 GLU cc_start: 0.8489 (tp30) cc_final: 0.8237 (tp30)
REVERT: B  442 ILE cc_start: 0.8805 (tp) cc_final: 0.8523 (mm)
REVERT: B  445 ARG cc_start: 0.8402 (ttt90) cc_final: 0.7920 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1902
  time to fit residues: 34.0096
Evaluate side-chains
  105 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 23 optimal weight:   20.0000
   chunk 60 optimal weight:    0.6980
   chunk 63 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 20 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 120 HIS
B 632 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.150723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.123807 restraints weight = 12792.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.127039 restraints weight = 7205.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.129022 restraints weight = 5002.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5072  Z= 0.245
  Angle     :  0.738   7.833   7024  Z= 0.353
  Chirality :  0.044   0.335    964
  Planarity :  0.005   0.078    812
  Dihedral  :  8.334  65.295   1629
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.52 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  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: -1.32 (0.33), residues: 670
  helix:  0.24 (0.26), residues: 388
  sheet: -0.52 (0.91), residues: 37
  loop : -2.80 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 146 
 HIS   0.022   0.004   HIS B 632 
 PHE   0.026   0.002   PHE B 420 
 TYR   0.020   0.002   TYR A 178 
 ARG   0.004   0.001   ARG A 103 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7432 (ptp-170)
REVERT: A  132 GLN cc_start: 0.6279 (mm110) cc_final: 0.5964 (mm110)
REVERT: A  209 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8027 (tp-100)
REVERT: B   16 TYR cc_start: 0.8282 (t80) cc_final: 0.7740 (t80)
REVERT: B   40 CYS cc_start: 0.6430 (m) cc_final: 0.6086 (m)
REVERT: B  378 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8198 (ttmm)
REVERT: B  383 GLN cc_start: 0.9095 (tt0) cc_final: 0.8684 (mt0)
REVERT: B  388 GLU cc_start: 0.8687 (tp30) cc_final: 0.8406 (tp30)
REVERT: B  396 MET cc_start: 0.7605 (ttm) cc_final: 0.7396 (ttm)
REVERT: B  415 GLN cc_start: 0.7934 (mt0) cc_final: 0.7592 (mt0)
REVERT: B  442 ILE cc_start: 0.8768 (tp) cc_final: 0.8498 (mm)
REVERT: B  445 ARG cc_start: 0.8336 (ttt90) cc_final: 0.7749 (mmm160)
REVERT: B  641 ASN cc_start: 0.5571 (t0) cc_final: 0.5301 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1808
  time to fit residues: 28.9630
Evaluate side-chains
  109 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0040
   chunk 28 optimal weight:    6.9990
   chunk 24 optimal weight:    0.4980
   chunk 46 optimal weight:    0.5980
   chunk 65 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:   30.0000
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A 120 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.152752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.127039 restraints weight = 13016.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.130205 restraints weight = 7246.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.131983 restraints weight = 5015.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5072  Z= 0.175
  Angle     :  0.678   7.326   7024  Z= 0.325
  Chirality :  0.042   0.311    964
  Planarity :  0.005   0.080    812
  Dihedral  :  7.814  63.119   1629
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.22 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.33), residues: 670
  helix:  0.52 (0.26), residues: 390
  sheet: -0.39 (0.92), residues: 37
  loop : -2.58 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.006   0.002   HIS B 632 
 PHE   0.011   0.001   PHE B 435 
 TYR   0.011   0.001   TYR B 639 
 ARG   0.003   0.000   ARG A 103 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7409 (ptp-170)
REVERT: A  132 GLN cc_start: 0.6044 (mm110) cc_final: 0.5743 (mm110)
REVERT: A  209 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8018 (tp-100)
REVERT: B   16 TYR cc_start: 0.8174 (t80) cc_final: 0.7627 (t80)
REVERT: B   17 ASN cc_start: 0.8901 (p0) cc_final: 0.8470 (t0)
REVERT: B  347 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7253 (mt-10)
REVERT: B  362 LEU cc_start: 0.8667 (mt) cc_final: 0.7824 (tt)
REVERT: B  378 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8220 (ttmm)
REVERT: B  380 ARG cc_start: 0.8360 (ttt90) cc_final: 0.7982 (ttt-90)
REVERT: B  383 GLN cc_start: 0.9014 (tt0) cc_final: 0.8665 (mt0)
REVERT: B  396 MET cc_start: 0.7391 (ttm) cc_final: 0.7171 (ttm)
REVERT: B  442 ILE cc_start: 0.8766 (tp) cc_final: 0.8546 (mm)
REVERT: B  445 ARG cc_start: 0.8155 (ttt90) cc_final: 0.7943 (ttt-90)
REVERT: B  641 ASN cc_start: 0.5307 (t0) cc_final: 0.5054 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1870
  time to fit residues: 32.9805
Evaluate side-chains
  112 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 66 optimal weight:   30.0000
   chunk 63 optimal weight:    0.0040
   chunk 46 optimal weight:    0.0010
   chunk 12 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 8 optimal weight:   20.0000
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
A 120 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.152410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.126996 restraints weight = 12890.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130257 restraints weight = 7102.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.132242 restraints weight = 4869.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5072  Z= 0.169
  Angle     :  0.652   9.788   7024  Z= 0.310
  Chirality :  0.041   0.304    964
  Planarity :  0.004   0.036    812
  Dihedral  :  7.456  61.135   1629
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.22 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.33), residues: 670
  helix:  0.81 (0.26), residues: 392
  sheet: -0.28 (0.94), residues: 37
  loop : -2.51 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.007   0.001   HIS B 632 
 PHE   0.014   0.002   PHE B  15 
 TYR   0.009   0.001   TYR B 300 
 ARG   0.002   0.000   ARG A 103 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7513 (ptp-170)
REVERT: A  132 GLN cc_start: 0.6222 (mm110) cc_final: 0.5714 (mm110)
REVERT: A  203 MET cc_start: 0.9054 (mtp) cc_final: 0.8790 (mtt)
REVERT: A  209 GLN cc_start: 0.8710 (tp-100) cc_final: 0.8294 (tp-100)
REVERT: B   16 TYR cc_start: 0.8146 (t80) cc_final: 0.7773 (t80)
REVERT: B  300 TYR cc_start: 0.8176 (t80) cc_final: 0.7968 (t80)
REVERT: B  347 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7302 (mt-10)
REVERT: B  359 GLU cc_start: 0.7644 (mp0) cc_final: 0.7404 (mp0)
REVERT: B  362 LEU cc_start: 0.8627 (mt) cc_final: 0.7820 (tt)
REVERT: B  383 GLN cc_start: 0.9070 (tt0) cc_final: 0.8723 (mt0)
REVERT: B  388 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7887 (mm-30)
REVERT: B  396 MET cc_start: 0.7390 (ttm) cc_final: 0.7045 (ttm)
REVERT: B  442 ILE cc_start: 0.8732 (tp) cc_final: 0.8500 (mm)
REVERT: B  641 ASN cc_start: 0.5168 (t0) cc_final: 0.4936 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1711
  time to fit residues: 29.1092
Evaluate side-chains
  109 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0670
   chunk 53 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.5920

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

Flipped N/Q/H residues before XYZ refinement:
A 120 HIS
B 432 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.152713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.125703 restraints weight = 12709.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.129140 restraints weight = 6953.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.131319 restraints weight = 4770.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.5046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5072  Z= 0.169
  Angle     :  0.643   6.309   7024  Z= 0.309
  Chirality :  0.042   0.300    964
  Planarity :  0.004   0.036    812
  Dihedral  :  7.322  59.842   1629
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.37 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  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: -0.38 (0.34), residues: 670
  helix:  1.00 (0.27), residues: 391
  sheet: -0.24 (0.93), residues: 37
  loop : -2.42 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.001   0.000   HIS A  99 
 PHE   0.017   0.001   PHE B 436 
 TYR   0.016   0.001   TYR A 180 
 ARG   0.003   0.000   ARG A 103 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7545 (ptp-170)
REVERT: A  120 HIS cc_start: 0.8449 (t-90) cc_final: 0.8078 (t-170)
REVERT: A  132 GLN cc_start: 0.6091 (mm110) cc_final: 0.5556 (mm110)
REVERT: A  166 THR cc_start: 0.9130 (m) cc_final: 0.8609 (m)
REVERT: A  170 GLN cc_start: 0.8420 (pm20) cc_final: 0.7510 (pm20)
REVERT: A  203 MET cc_start: 0.9226 (mtp) cc_final: 0.9004 (mtt)
REVERT: A  209 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8207 (tp-100)
REVERT: B   16 TYR cc_start: 0.8248 (t80) cc_final: 0.7845 (t80)
REVERT: B  347 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7361 (tp30)
REVERT: B  359 GLU cc_start: 0.7644 (mp0) cc_final: 0.7371 (mp0)
REVERT: B  362 LEU cc_start: 0.8507 (mt) cc_final: 0.7679 (tt)
REVERT: B  383 GLN cc_start: 0.9067 (tt0) cc_final: 0.8754 (mt0)
REVERT: B  442 ILE cc_start: 0.8817 (tp) cc_final: 0.8611 (mm)
REVERT: B  630 PHE cc_start: 0.7650 (t80) cc_final: 0.7317 (m-80)
REVERT: B  639 TYR cc_start: 0.8824 (m-10) cc_final: 0.8620 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1690
  time to fit residues: 29.8461
Evaluate side-chains
  116 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 66 optimal weight:   40.0000
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0670
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7522

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 120 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.152980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.125678 restraints weight = 12697.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.128898 restraints weight = 7181.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.130970 restraints weight = 5032.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.5306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5072  Z= 0.179
  Angle     :  0.663  10.023   7024  Z= 0.317
  Chirality :  0.042   0.299    964
  Planarity :  0.003   0.037    812
  Dihedral  :  7.311  59.499   1629
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.22 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.34), residues: 670
  helix:  1.09 (0.27), residues: 393
  sheet: -0.19 (0.93), residues: 37
  loop : -2.32 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.002   0.001   HIS B  18 
 PHE   0.014   0.001   PHE B 436 
 TYR   0.011   0.001   TYR A 178 
 ARG   0.003   0.000   ARG A 103 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.7595 (m) cc_final: 0.7306 (p)
REVERT: A   31 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7599 (ptp-170)
REVERT: A  103 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7357 (tpp80)
REVERT: A  132 GLN cc_start: 0.6181 (mm110) cc_final: 0.5733 (tt0)
REVERT: A  166 THR cc_start: 0.9242 (m) cc_final: 0.8950 (m)
REVERT: A  170 GLN cc_start: 0.8472 (pm20) cc_final: 0.7880 (pm20)
REVERT: A  203 MET cc_start: 0.9178 (mtp) cc_final: 0.8874 (mtp)
REVERT: B   16 TYR cc_start: 0.8253 (t80) cc_final: 0.7852 (t80)
REVERT: B  347 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7434 (tp30)
REVERT: B  359 GLU cc_start: 0.7552 (mp0) cc_final: 0.7266 (mp0)
REVERT: B  362 LEU cc_start: 0.8487 (mt) cc_final: 0.7677 (tt)
REVERT: B  378 LYS cc_start: 0.8958 (mttm) cc_final: 0.8636 (mmtt)
REVERT: B  383 GLN cc_start: 0.9039 (tt0) cc_final: 0.8747 (mt0)
REVERT: B  442 ILE cc_start: 0.8839 (tp) cc_final: 0.8612 (mm)
REVERT: B  630 PHE cc_start: 0.7661 (t80) cc_final: 0.7309 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1738
  time to fit residues: 29.8190
Evaluate side-chains
  115 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 36 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 25 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 120 HIS
** B 415 GLN ** 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 = 0.4050 r_free = 0.4050 target = 0.152273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.124407 restraints weight = 12888.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.127816 restraints weight = 7207.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.130057 restraints weight = 5001.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.5534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5072  Z= 0.182
  Angle     :  0.655   6.920   7024  Z= 0.316
  Chirality :  0.042   0.298    964
  Planarity :  0.003   0.036    812
  Dihedral  :  7.194  59.125   1629
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  4.78 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  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: -0.15 (0.34), residues: 670
  helix:  1.13 (0.27), residues: 393
  sheet: -0.23 (0.92), residues: 37
  loop : -2.23 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.004   0.001   HIS A 120 
 PHE   0.015   0.001   PHE B 436 
 TYR   0.029   0.001   TYR A  88 
 ARG   0.002   0.000   ARG B 445 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.7645 (m) cc_final: 0.7378 (p)
REVERT: A   31 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7600 (ptp-170)
REVERT: A  120 HIS cc_start: 0.8465 (t-90) cc_final: 0.8116 (t-170)
REVERT: A  132 GLN cc_start: 0.6217 (mm110) cc_final: 0.5902 (tt0)
REVERT: A  203 MET cc_start: 0.9064 (mtp) cc_final: 0.8823 (mtp)
REVERT: B   16 TYR cc_start: 0.8247 (t80) cc_final: 0.7835 (t80)
REVERT: B  308 MET cc_start: 0.6823 (mtt) cc_final: 0.6523 (mtm)
REVERT: B  347 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7407 (tp30)
REVERT: B  359 GLU cc_start: 0.7535 (mp0) cc_final: 0.7288 (mp0)
REVERT: B  362 LEU cc_start: 0.8487 (mt) cc_final: 0.7712 (tt)
REVERT: B  378 LYS cc_start: 0.9126 (mttm) cc_final: 0.8780 (mtpp)
REVERT: B  415 GLN cc_start: 0.7431 (mt0) cc_final: 0.7146 (mp10)
REVERT: B  630 PHE cc_start: 0.7669 (t80) cc_final: 0.7331 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1712
  time to fit residues: 30.1463
Evaluate side-chains
  111 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 2 optimal weight:    0.3980
   chunk 32 optimal weight:   20.0000
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 6 optimal weight:    0.2980
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 120 HIS
** B 415 GLN ** 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 = 0.4018 r_free = 0.4018 target = 0.149225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.121599 restraints weight = 12543.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.124874 restraints weight = 7063.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.126794 restraints weight = 5034.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.5758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5072  Z= 0.240
  Angle     :  0.696   6.959   7024  Z= 0.342
  Chirality :  0.044   0.320    964
  Planarity :  0.004   0.036    812
  Dihedral  :  7.333  59.995   1629
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.82 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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: -0.21 (0.34), residues: 670
  helix:  1.03 (0.27), residues: 396
  sheet: -0.31 (0.91), residues: 37
  loop : -2.18 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.002   0.001   HIS B  18 
 PHE   0.017   0.002   PHE B 436 
 TYR   0.028   0.002   TYR A  88 
 ARG   0.003   0.000   ARG A 103 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.7694 (m) cc_final: 0.7399 (p)
REVERT: A   31 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7808 (ptp-170)
REVERT: A  132 GLN cc_start: 0.6329 (mm110) cc_final: 0.6084 (tt0)
REVERT: A  209 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8193 (tp-100)
REVERT: B   16 TYR cc_start: 0.8368 (t80) cc_final: 0.7970 (t80)
REVERT: B  359 GLU cc_start: 0.7576 (mp0) cc_final: 0.7282 (mp0)
REVERT: B  362 LEU cc_start: 0.8521 (mt) cc_final: 0.7787 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1657
  time to fit residues: 28.6322
Evaluate side-chains
  112 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 4 optimal weight:    0.1980
   chunk 3 optimal weight:    0.0770
   chunk 22 optimal weight:    0.0270
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 120 HIS
** B 415 GLN ** 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 = 0.4031 r_free = 0.4031 target = 0.150876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123215 restraints weight = 12638.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.126702 restraints weight = 7106.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.128839 restraints weight = 4977.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.6027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5072  Z= 0.178
  Angle     :  0.692   8.469   7024  Z= 0.336
  Chirality :  0.043   0.292    964
  Planarity :  0.004   0.038    812
  Dihedral  :  7.105  58.744   1629
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  4.93 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.54 %
    Favored  : 99.18 %
  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 (0.34), residues: 670
  helix:  1.15 (0.27), residues: 396
  sheet: -0.25 (0.92), residues: 37
  loop : -2.11 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 633 
 HIS   0.003   0.001   HIS A 120 
 PHE   0.016   0.001   PHE B 436 
 TYR   0.023   0.001   TYR A  88 
 ARG   0.005   0.001   ARG B  13 

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

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

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1340 Ramachandran restraints generated.
    670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.7635 (m) cc_final: 0.7356 (p)
REVERT: A   31 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7771 (ptp-170)
REVERT: A  132 GLN cc_start: 0.6275 (mm110) cc_final: 0.5944 (tt0)
REVERT: A  205 ASN cc_start: 0.9098 (t0) cc_final: 0.8652 (t0)
REVERT: A  209 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8243 (tp-100)
REVERT: B   16 TYR cc_start: 0.8406 (t80) cc_final: 0.7953 (t80)
REVERT: B  359 GLU cc_start: 0.7463 (mp0) cc_final: 0.7117 (mp0)
REVERT: B  362 LEU cc_start: 0.8478 (mt) cc_final: 0.7744 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1579
  time to fit residues: 28.8181
Evaluate side-chains
  112 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 29 optimal weight:   40.0000
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 54 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0670
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:   40.0000
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 120 HIS
** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.150492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.122853 restraints weight = 12648.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.126113 restraints weight = 7300.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.128143 restraints weight = 5169.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.6181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5072  Z= 0.186
  Angle     :  0.674   7.901   7024  Z= 0.331
  Chirality :  0.042   0.299    964
  Planarity :  0.004   0.037    812
  Dihedral  :  7.029  59.500   1629
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.37 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  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: -0.01 (0.35), residues: 670
  helix:  1.17 (0.27), residues: 401
  sheet: -0.21 (0.93), residues: 37
  loop : -2.13 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 633 
 HIS   0.007   0.002   HIS A  99 
 PHE   0.026   0.002   PHE B 429 
 TYR   0.023   0.001   TYR A  88 
 ARG   0.004   0.000   ARG B  13 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1887.40 seconds
wall clock time: 34 minutes 20.38 seconds (2060.38 seconds total)