Starting phenix.real_space_refine
on Thu Mar  6 07:33:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7etw_31303/03_2025/7etw_31303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7etw_31303/03_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_31303/03_2025/7etw_31303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7etw_31303/03_2025/7etw_31303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7etw_31303/03_2025/7etw_31303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7etw_31303/03_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-5624/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: 3.81, per 1000 atoms: 0.77
  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: 1.56
  Conformation dependent library (CDL) restraints added in 797.6 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: 0.49
  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: 1.29

  Time building geometry restraints manager: 1.79 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.720
  Find NCS groups from input model:        0.040
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.650
-------------------------------------------------------------------------------
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  : 0.493 
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: 0.1994
  time to fit residues: 38.9336
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  : 0.546 
-------------------------------------------------------------------------------
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 = 0.152811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.125718 restraints weight = 11626.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.129197 restraints weight = 6378.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.131357 restraints weight = 4344.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2981

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= 0.273
  Angle     :  0.832   7.707   7024  Z= 0.397
  Chirality :  0.047   0.361    964
  Planarity :  0.006   0.088    812
  Dihedral  :  9.315  68.267   1629
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.25
  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   0.022   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  : 0.546 
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: 0.7683 (mtm-85) cc_final: 0.7197 (ptp-170)
REVERT: A  209 GLN cc_start: 0.8405 (tp-100) cc_final: 0.7762 (tp-100)
REVERT: B  298 TYR cc_start: 0.8677 (t80) cc_final: 0.8188 (t80)
REVERT: B  347 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7552 (mt-10)
REVERT: B  378 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8169 (ttmm)
REVERT: B  380 ARG cc_start: 0.8465 (ttt90) cc_final: 0.8184 (ttt180)
REVERT: B  383 GLN cc_start: 0.9095 (tt0) cc_final: 0.8583 (mt0)
REVERT: B  388 GLU cc_start: 0.8492 (tp30) cc_final: 0.8242 (tp30)
REVERT: B  442 ILE cc_start: 0.8815 (tp) cc_final: 0.8532 (mm)
REVERT: B  445 ARG cc_start: 0.8393 (ttt90) cc_final: 0.7911 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1828
  time to fit residues: 32.3386
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  : 0.500 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 53 optimal weight:   20.0000
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.4050 r_free = 0.4050 target = 0.152070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.125564 restraints weight = 12751.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.128824 restraints weight = 7043.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.130901 restraints weight = 4848.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.3793

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= 0.220
  Angle     :  0.722   7.745   7024  Z= 0.344
  Chirality :  0.044   0.327    964
  Planarity :  0.005   0.077    812
  Dihedral  :  8.300  65.307   1629
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.67 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  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: -1.29 (0.33), residues: 670
  helix:  0.28 (0.26), residues: 388
  sheet: -0.57 (0.90), residues: 37
  loop : -2.80 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 146 
 HIS   0.022   0.003   HIS B 632 
 PHE   0.022   0.002   PHE B 420 
 TYR   0.018   0.002   TYR A 178 
 ARG   0.004   0.001   ARG B 631 

*********************** 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
  126 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.424 
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: 0.7681 (mtm-85) cc_final: 0.7358 (ptp-170)
REVERT: A  132 GLN cc_start: 0.6236 (mm110) cc_final: 0.5919 (mm110)
REVERT: A  166 THR cc_start: 0.9146 (m) cc_final: 0.8642 (m)
REVERT: A  170 GLN cc_start: 0.8546 (pm20) cc_final: 0.7812 (pm20)
REVERT: A  209 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8060 (tp-100)
REVERT: B   40 CYS cc_start: 0.6325 (m) cc_final: 0.5971 (m)
REVERT: B  298 TYR cc_start: 0.8844 (t80) cc_final: 0.8642 (t80)
REVERT: B  329 MET cc_start: 0.8134 (mtp) cc_final: 0.7876 (mtm)
REVERT: B  347 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7433 (mt-10)
REVERT: B  378 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8196 (ttmm)
REVERT: B  383 GLN cc_start: 0.9056 (tt0) cc_final: 0.8637 (mt0)
REVERT: B  388 GLU cc_start: 0.8658 (tp30) cc_final: 0.8368 (tp30)
REVERT: B  396 MET cc_start: 0.7541 (ttm) cc_final: 0.7294 (ttm)
REVERT: B  442 ILE cc_start: 0.8750 (tp) cc_final: 0.8483 (mm)
REVERT: B  445 ARG cc_start: 0.8347 (ttt90) cc_final: 0.7761 (mmm160)
REVERT: B  641 ASN cc_start: 0.5363 (t0) cc_final: 0.5074 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1710
  time to fit residues: 27.5167
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  : 0.525 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0370
   chunk 46 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 51 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:   30.0000
   overall best weight:    0.7262

-------------------------------------------------------------------------------
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 = 0.152760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.126360 restraints weight = 13017.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.129672 restraints weight = 7183.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.131857 restraints weight = 4885.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5072  Z= 0.186
  Angle     :  0.680   8.266   7024  Z= 0.325
  Chirality :  0.042   0.316    964
  Planarity :  0.004   0.045    812
  Dihedral  :  7.853  63.415   1629
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.37 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  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: -0.96 (0.33), residues: 670
  helix:  0.52 (0.26), residues: 391
  sheet: -0.42 (0.91), residues: 37
  loop : -2.65 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 146 
 HIS   0.005   0.002   HIS B 632 
 PHE   0.012   0.001   PHE B 435 
 TYR   0.010   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
  137 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7389 (ptp-170)
REVERT: A   92 ASP cc_start: 0.7757 (t0) cc_final: 0.7516 (t0)
REVERT: A  103 ARG cc_start: 0.7893 (tpp80) cc_final: 0.7577 (tpp80)
REVERT: A  132 GLN cc_start: 0.6101 (mm110) cc_final: 0.5768 (mm110)
REVERT: A  209 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8069 (tp-100)
REVERT: B   16 TYR cc_start: 0.8227 (t80) cc_final: 0.7642 (t80)
REVERT: B   17 ASN cc_start: 0.8934 (p0) cc_final: 0.8513 (t0)
REVERT: B   40 CYS cc_start: 0.6305 (m) cc_final: 0.6039 (m)
REVERT: B  298 TYR cc_start: 0.8935 (t80) cc_final: 0.8527 (t80)
REVERT: B  329 MET cc_start: 0.8036 (mtp) cc_final: 0.7831 (mtm)
REVERT: B  347 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7455 (mt-10)
REVERT: B  362 LEU cc_start: 0.8684 (mt) cc_final: 0.7956 (tt)
REVERT: B  383 GLN cc_start: 0.9052 (tt0) cc_final: 0.8702 (mt0)
REVERT: B  396 MET cc_start: 0.7410 (ttm) cc_final: 0.7164 (ttm)
REVERT: B  442 ILE cc_start: 0.8765 (tp) cc_final: 0.8535 (mm)
REVERT: B  445 ARG cc_start: 0.8162 (ttt90) cc_final: 0.7959 (ttt-90)
REVERT: B  641 ASN cc_start: 0.5311 (t0) cc_final: 0.5046 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1673
  time to fit residues: 28.8645
Evaluate side-chains
  110 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 31 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0000
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 52 optimal weight:    0.1980
   chunk 18 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.4184

-------------------------------------------------------------------------------
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 = 0.4067 r_free = 0.4067 target = 0.153408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.126008 restraints weight = 12897.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.129381 restraints weight = 7065.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.131488 restraints weight = 4864.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5072  Z= 0.168
  Angle     :  0.650   9.459   7024  Z= 0.311
  Chirality :  0.041   0.303    964
  Planarity :  0.004   0.039    812
  Dihedral  :  7.488  61.291   1629
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  4.78 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  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: -0.63 (0.33), residues: 670
  helix:  0.79 (0.27), residues: 392
  sheet: -0.30 (0.93), residues: 37
  loop : -2.54 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.007   0.002   HIS B 632 
 PHE   0.016   0.001   PHE B 436 
 TYR   0.008   0.001   TYR A 178 
 ARG   0.002   0.000   ARG B  13 

*********************** 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
  138 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  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: symmetry clash
REVERT: A   31 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7500 (ptp-170)
REVERT: A   92 ASP cc_start: 0.7800 (t0) cc_final: 0.7556 (t0)
REVERT: A  103 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7261 (mmt90)
REVERT: A  132 GLN cc_start: 0.6395 (mm110) cc_final: 0.5857 (mm110)
REVERT: A  149 ASP cc_start: 0.8630 (t0) cc_final: 0.8296 (t70)
REVERT: A  209 GLN cc_start: 0.8816 (tp-100) cc_final: 0.7999 (tp-100)
REVERT: B   16 TYR cc_start: 0.8247 (t80) cc_final: 0.7669 (t80)
REVERT: B   40 CYS cc_start: 0.6217 (m) cc_final: 0.5986 (m)
REVERT: B  298 TYR cc_start: 0.8937 (t80) cc_final: 0.8494 (t80)
REVERT: B  329 MET cc_start: 0.8114 (mtp) cc_final: 0.7891 (mtm)
REVERT: B  347 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7513 (mt-10)
REVERT: B  359 GLU cc_start: 0.7679 (mp0) cc_final: 0.7438 (mp0)
REVERT: B  362 LEU cc_start: 0.8587 (mt) cc_final: 0.7819 (tt)
REVERT: B  378 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8509 (ttmm)
REVERT: B  383 GLN cc_start: 0.9120 (tt0) cc_final: 0.8738 (mt0)
REVERT: B  396 MET cc_start: 0.7332 (ttm) cc_final: 0.7098 (ttm)
REVERT: B  442 ILE cc_start: 0.8789 (tp) cc_final: 0.8550 (mm)
REVERT: B  641 ASN cc_start: 0.5119 (t0) cc_final: 0.4882 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1788
  time to fit residues: 31.1345
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  : 0.545 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 37 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.150748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.122649 restraints weight = 12744.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.125946 restraints weight = 7212.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.127987 restraints weight = 5072.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.4984

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= 0.227
  Angle     :  0.671   6.605   7024  Z= 0.323
  Chirality :  0.043   0.319    964
  Planarity :  0.004   0.037    812
  Dihedral  :  7.457  59.793   1629
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  6.27 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  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: -0.47 (0.34), residues: 670
  helix:  0.86 (0.27), residues: 392
  sheet: -0.24 (0.93), residues: 37
  loop : -2.34 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.009   0.002   HIS B 632 
 PHE   0.018   0.002   PHE B 436 
 TYR   0.015   0.002   TYR A 178 
 ARG   0.001   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
  138 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7686 (ptp-170)
REVERT: A   92 ASP cc_start: 0.8036 (t0) cc_final: 0.7701 (t0)
REVERT: A  103 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7469 (mmt90)
REVERT: A  120 HIS cc_start: 0.8545 (t-90) cc_final: 0.8270 (t-170)
REVERT: A  132 GLN cc_start: 0.6251 (mm110) cc_final: 0.5826 (tt0)
REVERT: A  149 ASP cc_start: 0.8325 (t0) cc_final: 0.7904 (t70)
REVERT: A  164 LEU cc_start: 0.7629 (mm) cc_final: 0.6908 (tt)
REVERT: A  166 THR cc_start: 0.9201 (m) cc_final: 0.8704 (m)
REVERT: A  170 GLN cc_start: 0.8399 (pm20) cc_final: 0.7487 (pm20)
REVERT: A  203 MET cc_start: 0.9145 (mtp) cc_final: 0.8937 (mtp)
REVERT: A  209 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8103 (tp-100)
REVERT: B   16 TYR cc_start: 0.8291 (t80) cc_final: 0.7945 (t80)
REVERT: B   40 CYS cc_start: 0.6226 (m) cc_final: 0.5949 (m)
REVERT: B  298 TYR cc_start: 0.9068 (t80) cc_final: 0.8691 (t80)
REVERT: B  329 MET cc_start: 0.8149 (mtp) cc_final: 0.7892 (mtm)
REVERT: B  347 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7266 (tp30)
REVERT: B  359 GLU cc_start: 0.7722 (mp0) cc_final: 0.7478 (mp0)
REVERT: B  362 LEU cc_start: 0.8576 (mt) cc_final: 0.7799 (tt)
REVERT: B  383 GLN cc_start: 0.9113 (tt0) cc_final: 0.8797 (mt0)
REVERT: B  442 ILE cc_start: 0.8860 (tp) cc_final: 0.8622 (mm)
REVERT: B  641 ASN cc_start: 0.5200 (t0) cc_final: 0.4953 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1755
  time to fit residues: 30.4738
Evaluate side-chains
  118 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 66 optimal weight:   40.0000
   chunk 49 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.151508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.123788 restraints weight = 12660.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.126970 restraints weight = 7213.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.129157 restraints weight = 5107.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.5249

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= 0.181
  Angle     :  0.673   6.963   7024  Z= 0.322
  Chirality :  0.042   0.304    964
  Planarity :  0.004   0.039    812
  Dihedral  :  7.395  59.789   1629
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.52 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.34), residues: 670
  helix:  1.03 (0.27), residues: 393
  sheet: -0.08 (0.94), residues: 37
  loop : -2.32 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.003   0.001   HIS A 120 
 PHE   0.017   0.001   PHE B 430 
 TYR   0.028   0.002   TYR B 639 
 ARG   0.002   0.000   ARG A 208 

*********************** 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
  138 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  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: A   22 THR cc_start: 0.7635 (m) cc_final: 0.7341 (p)
REVERT: A   31 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7612 (ptp-170)
REVERT: A  103 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7441 (mmt90)
REVERT: A  132 GLN cc_start: 0.6159 (mm110) cc_final: 0.5806 (tt0)
REVERT: A  166 THR cc_start: 0.9250 (m) cc_final: 0.8965 (m)
REVERT: A  170 GLN cc_start: 0.8436 (pm20) cc_final: 0.7825 (pm20)
REVERT: A  203 MET cc_start: 0.9129 (mtp) cc_final: 0.8878 (mtp)
REVERT: A  208 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8537 (mtm180)
REVERT: B   16 TYR cc_start: 0.8163 (t80) cc_final: 0.7812 (t80)
REVERT: B  298 TYR cc_start: 0.9100 (t80) cc_final: 0.8623 (t80)
REVERT: B  347 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7265 (tp30)
REVERT: B  359 GLU cc_start: 0.7600 (mp0) cc_final: 0.7369 (mp0)
REVERT: B  362 LEU cc_start: 0.8535 (mt) cc_final: 0.7773 (tt)
REVERT: B  378 LYS cc_start: 0.8875 (mttm) cc_final: 0.8544 (mmmt)
REVERT: B  383 GLN cc_start: 0.9007 (tt0) cc_final: 0.8722 (mt0)
REVERT: B  442 ILE cc_start: 0.8828 (tp) cc_final: 0.8596 (mm)
REVERT: B  630 PHE cc_start: 0.7569 (t80) cc_final: 0.7289 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1753
  time to fit residues: 30.5479
Evaluate side-chains
  117 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 36 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0670
   chunk 55 optimal weight:    0.8980
   chunk 25 optimal weight:   30.0000
   chunk 11 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.4043 r_free = 0.4043 target = 0.151102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.123785 restraints weight = 12777.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.127354 restraints weight = 6970.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.129620 restraints weight = 4784.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.5413

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= 0.171
  Angle     :  0.665   6.682   7024  Z= 0.322
  Chirality :  0.042   0.295    964
  Planarity :  0.004   0.040    812
  Dihedral  :  7.232  59.432   1629
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.07 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  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: -0.12 (0.34), residues: 670
  helix:  1.14 (0.27), residues: 393
  sheet: -0.10 (0.93), residues: 37
  loop : -2.22 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.003   0.001   HIS B 632 
 PHE   0.018   0.001   PHE B 420 
 TYR   0.009   0.001   TYR A 180 
 ARG   0.002   0.000   ARG A 208 

*********************** 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
  144 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.585 
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: 0.7650 (m) cc_final: 0.7370 (p)
REVERT: A   31 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7697 (ptp-170)
REVERT: A  120 HIS cc_start: 0.8491 (t-90) cc_final: 0.8132 (t-170)
REVERT: A  132 GLN cc_start: 0.6229 (mm110) cc_final: 0.5774 (tt0)
REVERT: A  203 MET cc_start: 0.9207 (mtp) cc_final: 0.8992 (mtp)
REVERT: B   16 TYR cc_start: 0.8241 (t80) cc_final: 0.7870 (t80)
REVERT: B  298 TYR cc_start: 0.9067 (t80) cc_final: 0.8443 (t80)
REVERT: B  347 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7310 (tp30)
REVERT: B  359 GLU cc_start: 0.7634 (mp0) cc_final: 0.7393 (mp0)
REVERT: B  362 LEU cc_start: 0.8473 (mt) cc_final: 0.7791 (tt)
REVERT: B  378 LYS cc_start: 0.9125 (mttm) cc_final: 0.8552 (mmmt)
REVERT: B  383 GLN cc_start: 0.9065 (tt0) cc_final: 0.8842 (mt0)
REVERT: B  415 GLN cc_start: 0.7722 (mt0) cc_final: 0.7509 (mt0)
REVERT: B  630 PHE cc_start: 0.7547 (t80) cc_final: 0.7292 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1638
  time to fit residues: 30.0042
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  : 0.499 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:   30.0000
   chunk 42 optimal weight:    9.9990
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4049 r_free = 0.4049 target = 0.151721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.124309 restraints weight = 12572.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.127682 restraints weight = 7087.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.129759 restraints weight = 4998.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.5622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5072  Z= 0.169
  Angle     :  0.653   6.492   7024  Z= 0.315
  Chirality :  0.042   0.295    964
  Planarity :  0.003   0.034    812
  Dihedral  :  7.114  58.829   1629
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.07 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  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: -0.01 (0.34), residues: 670
  helix:  1.24 (0.27), residues: 396
  sheet: -0.10 (0.93), residues: 37
  loop : -2.21 (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   0.025   0.001   PHE B 435 
 TYR   0.009   0.001   TYR B 351 
 ARG   0.002   0.000   ARG A 208 

*********************** 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
  139 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.587 
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: 0.7657 (m) cc_final: 0.7366 (p)
REVERT: A   31 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7687 (ptp-170)
REVERT: A  103 ARG cc_start: 0.7383 (tpp80) cc_final: 0.7054 (mmt90)
REVERT: A  120 HIS cc_start: 0.8421 (t70) cc_final: 0.8212 (t-170)
REVERT: A  132 GLN cc_start: 0.6212 (mm110) cc_final: 0.5960 (tt0)
REVERT: A  203 MET cc_start: 0.9137 (mtp) cc_final: 0.8907 (mtp)
REVERT: B   16 TYR cc_start: 0.8136 (t80) cc_final: 0.7778 (t80)
REVERT: B  298 TYR cc_start: 0.9056 (t80) cc_final: 0.8465 (t80)
REVERT: B  347 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7334 (tp30)
REVERT: B  359 GLU cc_start: 0.7537 (mp0) cc_final: 0.7308 (mp0)
REVERT: B  362 LEU cc_start: 0.8449 (mt) cc_final: 0.7736 (tt)
REVERT: B  378 LYS cc_start: 0.9133 (mttm) cc_final: 0.8922 (mtpp)
REVERT: B  447 MET cc_start: 0.7844 (ttt) cc_final: 0.6993 (ppp)
REVERT: B  630 PHE cc_start: 0.7538 (t80) cc_final: 0.7254 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1750
  time to fit residues: 30.6146
Evaluate side-chains
  117 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0000
   chunk 4 optimal weight:    0.0000
   chunk 3 optimal weight:    0.0370
   chunk 22 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.3466

-------------------------------------------------------------------------------
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**
B 415 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.153044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.125725 restraints weight = 12689.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.129201 restraints weight = 7089.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.131435 restraints weight = 4939.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.5770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5072  Z= 0.167
  Angle     :  0.668   8.139   7024  Z= 0.324
  Chirality :  0.042   0.288    964
  Planarity :  0.004   0.043    812
  Dihedral  :  6.977  58.514   1629
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.07 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.04 (0.34), residues: 670
  helix:  1.30 (0.27), residues: 398
  sheet: -0.12 (0.92), residues: 37
  loop : -2.26 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.003   0.001   HIS A  99 
 PHE   0.012   0.001   PHE A 197 
 TYR   0.009   0.001   TYR A  88 
 ARG   0.002   0.000   ARG A 208 

********************** 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
  143 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.507 
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: 0.7660 (m) cc_final: 0.7381 (p)
REVERT: A   31 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7695 (ptp-170)
REVERT: A  132 GLN cc_start: 0.6217 (mm110) cc_final: 0.5894 (tt0)
REVERT: A  203 MET cc_start: 0.9144 (mtp) cc_final: 0.8923 (mtp)
REVERT: B   16 TYR cc_start: 0.8229 (t80) cc_final: 0.7869 (t80)
REVERT: B  298 TYR cc_start: 0.8988 (t80) cc_final: 0.8273 (t80)
REVERT: B  308 MET cc_start: 0.7066 (mtt) cc_final: 0.6755 (mtm)
REVERT: B  347 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7344 (tp30)
REVERT: B  359 GLU cc_start: 0.7656 (mp0) cc_final: 0.7395 (mp0)
REVERT: B  362 LEU cc_start: 0.8442 (mt) cc_final: 0.7807 (tt)
REVERT: B  378 LYS cc_start: 0.9140 (mttm) cc_final: 0.8507 (mmmt)
REVERT: B  415 GLN cc_start: 0.7656 (mt0) cc_final: 0.7073 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1883
  time to fit residues: 33.7958
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  : 0.562 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 29 optimal weight:   40.0000
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 60 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:   40.0000
   chunk 38 optimal weight:    0.0010
   overall best weight:    1.3990

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.149386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.121326 restraints weight = 12697.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.124726 restraints weight = 7067.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.126857 restraints weight = 4922.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.5911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5072  Z= 0.220
  Angle     :  0.670   8.747   7024  Z= 0.328
  Chirality :  0.042   0.306    964
  Planarity :  0.004   0.038    812
  Dihedral  :  7.037  58.920   1629
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.07 %
    Favored  : 94.33 %
  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:  0.14 (0.35), residues: 670
  helix:  1.34 (0.27), residues: 398
  sheet: -0.18 (0.91), residues: 37
  loop : -2.12 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.003   0.001   HIS A 120 
 PHE   0.014   0.001   PHE A 197 
 TYR   0.010   0.001   TYR A 187 
 ARG   0.012   0.001   ARG A 103 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1900.81 seconds
wall clock time: 33 minutes 27.52 seconds (2007.52 seconds total)