Starting phenix.real_space_refine
on Wed Jul 30 15:42:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6s2e_10088/07_2025/6s2e_10088.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6s2e_10088/07_2025/6s2e_10088.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6s2e_10088/07_2025/6s2e_10088.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6s2e_10088/07_2025/6s2e_10088.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6s2e_10088/07_2025/6s2e_10088.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6s2e_10088/07_2025/6s2e_10088.cif"
  }
  resolution = 4.2
  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=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      68      5.16       5
     C    7984      2.51       5
     N    2079      2.21       5
     O    2324      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12459
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 8154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1006, 8154
          Classifications: {'peptide': 1006}
          Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 957}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 1031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1031
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "E"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 225
          Classifications: {'peptide': 26}
          Link IDs: {'TRANS': 25}
    Chain: "B"
      Number of atoms: 3041
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 3041
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 19, 'TRANS': 355}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4761  SG  CYS A 677      74.994  35.130  17.630  1.00143.72           S
  ATOM   4690  SG  CYS A 668      72.088  29.439  18.791  1.00135.31           S
  ATOM   4963  SG  CYS A 763      75.014  33.159  23.280  1.00114.07           S
  ATOM   4673  SG  CYS A 665      77.473  29.916  18.710  1.00136.78           S

  Time building chain proxies: 7.53, per 1000 atoms: 0.60
  Number of scatterers: 12459
  At special positions: 0
  Unit cell: (126.557, 128.684, 103.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      68     16.00
     O    2324      8.00
     N    2079      7.00
     C    7984      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
  Time building additional restraints: 2.77
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1401 "
        pdb="FE1  SF4 A1401 " - pdb=" SG  CYS A 677 "
        pdb="FE4  SF4 A1401 " - pdb=" SG  CYS A 665 "
        pdb="FE3  SF4 A1401 " - pdb=" SG  CYS A 763 "
        pdb="FE2  SF4 A1401 " - pdb=" SG  CYS A 668 "
      Number of angles added : 12


  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2924

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 0 sheets defined
      42.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 50
    Processing helix  chain 'A' and resid 145 through 147
      No H-bonds generated for 'chain 'A' and resid 145 through 147'
    Processing helix  chain 'A' and resid 148 through 160
    Processing helix  chain 'A' and resid 179 through 183
    Processing helix  chain 'A' and resid 195 through 212
      Proline residue:  A 208  - end of helix
    Processing helix  chain 'A' and resid 248 through 257
    Processing helix  chain 'A' and resid 354 through 370
    Processing helix  chain 'A' and resid 382 through 394
      removed outlier: 3.542A  pdb=" N   PHE A 386 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 403
    Processing helix  chain 'A' and resid 422 through 430
    Processing helix  chain 'A' and resid 433 through 437
    Processing helix  chain 'A' and resid 438 through 447
    Processing helix  chain 'A' and resid 455 through 466
      Proline residue:  A 461  - end of helix
      removed outlier: 4.051A  pdb=" N   PHE A 464 " --> pdb=" O   THR A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 498
      removed outlier: 3.618A  pdb=" N   LEU A 470 " --> pdb=" O   LYS A 466 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   HIS A 490 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      Proline residue:  A 491  - end of helix
    Processing helix  chain 'A' and resid 503 through 510
    Processing helix  chain 'A' and resid 511 through 527
    Processing helix  chain 'A' and resid 577 through 598
      removed outlier: 3.576A  pdb=" N   ILE A 581 " --> pdb=" O   ASP A 577 " (cutoff:3.500A)
      Proline residue:  A 589  - end of helix
    Processing helix  chain 'A' and resid 603 through 607
    Processing helix  chain 'A' and resid 609 through 627
    Processing helix  chain 'A' and resid 643 through 652
    Processing helix  chain 'A' and resid 655 through 659
    Processing helix  chain 'A' and resid 769 through 798
      removed outlier: 3.974A  pdb=" N   ILE A 798 " --> pdb=" O   ASN A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 834
      removed outlier: 3.710A  pdb=" N   PHE A 830 " --> pdb=" O   ILE A 826 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   TYR A 831 " --> pdb=" O   LEU A 827 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   GLY A 832 " --> pdb=" O   ASN A 828 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   VAL A 834 " --> pdb=" O   PHE A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 843 through 869
    Processing helix  chain 'A' and resid 905 through 919
      removed outlier: 3.868A  pdb=" N   THR A 919 " --> pdb=" O   HIS A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1006
      removed outlier: 4.731A  pdb=" N   LYS A1004 " --> pdb=" O   SER A1000 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   VAL A1005 " --> pdb=" O   ASP A1001 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   PHE A1006 " --> pdb=" O   ILE A1002 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1032
    Processing helix  chain 'A' and resid 1038 through 1045
      removed outlier: 3.608A  pdb=" N   LEU A1042 " --> pdb=" O   GLU A1038 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL A1043 " --> pdb=" O   ASP A1039 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER A1044 " --> pdb=" O   GLU A1040 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LEU A1045 " --> pdb=" O   ASP A1041 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1038 through 1045'
    Processing helix  chain 'A' and resid 1065 through 1078
      removed outlier: 3.575A  pdb=" N   THR A1069 " --> pdb=" O   THR A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1083
    Processing helix  chain 'A' and resid 1101 through 1105
    Processing helix  chain 'A' and resid 1137 through 1141
    Processing helix  chain 'A' and resid 1142 through 1158
    Processing helix  chain 'A' and resid 1158 through 1165
    Processing helix  chain 'A' and resid 1177 through 1184
      removed outlier: 3.812A  pdb=" N   LYS A1181 " --> pdb=" O   PRO A1177 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE A1184 " --> pdb=" O   LEU A1180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 18
    Processing helix  chain 'D' and resid 45 through 51
      removed outlier: 3.758A  pdb=" N   ARG D  50 " --> pdb=" O   ALA D  46 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG D  51 " --> pdb=" O   SER D  47 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 735 through 740
      removed outlier: 3.647A  pdb=" N   LEU E 739 " --> pdb=" O   THR E 735 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 29
    Processing helix  chain 'B' and resid 130 through 138
      removed outlier: 3.945A  pdb=" N   LYS B 134 " --> pdb=" O   ASP B 130 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   MET B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 153
    Processing helix  chain 'B' and resid 157 through 168
    Processing helix  chain 'B' and resid 181 through 199
    Processing helix  chain 'B' and resid 207 through 216
      removed outlier: 3.597A  pdb=" N   THR B 211 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 224
    Processing helix  chain 'B' and resid 227 through 238
    Processing helix  chain 'B' and resid 253 through 269
    Processing helix  chain 'B' and resid 277 through 288
      removed outlier: 3.987A  pdb=" N   PHE B 288 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 302
    Processing helix  chain 'B' and resid 317 through 321
    Processing helix  chain 'B' and resid 324 through 336
    Processing helix  chain 'B' and resid 340 through 349
      Proline residue:  B 346  - end of helix
    Processing helix  chain 'B' and resid 357 through 363

    401 hydrogen bonds defined for protein.
    1146 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.90

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.21 -     1.40: 5172
        1.40 -     1.59: 7448
        1.59 -     1.78: 8
        1.78 -     1.96: 99
        1.96 -     2.15: 12
  Bond restraints: 12739
  Sorted by residual:
  bond pdb=" S2  SF4 A1401 "
       pdb="FE4  SF4 A1401 "
    ideal  model  delta    sigma   weight residual
    2.280  2.098  0.182 3.00e-02 1.11e+03 3.68e+01
  bond pdb=" S4  SF4 A1401 "
       pdb="FE1  SF4 A1401 "
    ideal  model  delta    sigma   weight residual
    2.280  2.100  0.180 3.00e-02 1.11e+03 3.59e+01
  bond pdb=" S2  SF4 A1401 "
       pdb="FE3  SF4 A1401 "
    ideal  model  delta    sigma   weight residual
    2.280  2.117  0.163 3.00e-02 1.11e+03 2.95e+01
  bond pdb=" S3  SF4 A1401 "
       pdb="FE2  SF4 A1401 "
    ideal  model  delta    sigma   weight residual
    2.280  2.125  0.155 3.00e-02 1.11e+03 2.67e+01
  bond pdb=" S4  SF4 A1401 "
       pdb="FE3  SF4 A1401 "
    ideal  model  delta    sigma   weight residual
    2.280  2.126  0.154 3.00e-02 1.11e+03 2.62e+01
  ... (remaining 12734 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.68: 16925
        4.68 -     9.36: 266
        9.36 -    14.04: 20
       14.04 -    18.72: 6
       18.72 -    23.40: 3
  Bond angle restraints: 17220
  Sorted by residual:
  angle pdb=" CA  GLU A 623 "
        pdb=" CB  GLU A 623 "
        pdb=" CG  GLU A 623 "
      ideal   model   delta    sigma   weight residual
     114.10  128.77  -14.67 2.00e+00 2.50e-01 5.38e+01
  angle pdb=" CA  LEU A1045 "
        pdb=" CB  LEU A1045 "
        pdb=" CG  LEU A1045 "
      ideal   model   delta    sigma   weight residual
     116.30  139.70  -23.40 3.50e+00 8.16e-02 4.47e+01
  angle pdb=" C   GLU A 244 "
        pdb=" N   TYR A 245 "
        pdb=" CA  TYR A 245 "
      ideal   model   delta    sigma   weight residual
     122.26  111.53   10.73 1.73e+00 3.34e-01 3.85e+01
  angle pdb=" CA  LEU B  87 "
        pdb=" CB  LEU B  87 "
        pdb=" CG  LEU B  87 "
      ideal   model   delta    sigma   weight residual
     116.30  136.03  -19.73 3.50e+00 8.16e-02 3.18e+01
  angle pdb=" C   THR B 375 "
        pdb=" N   VAL B 376 "
        pdb=" CA  VAL B 376 "
      ideal   model   delta    sigma   weight residual
     122.48  116.28    6.20 1.13e+00 7.83e-01 3.01e+01
  ... (remaining 17215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 6970
       17.81 -    35.61: 603
       35.61 -    53.42: 115
       53.42 -    71.23: 27
       71.23 -    89.03: 8
  Dihedral angle restraints: 7723
    sinusoidal: 3214
      harmonic: 4509
  Sorted by residual:
  dihedral pdb=" CA  SER B 379 "
           pdb=" C   SER B 379 "
           pdb=" N   ARG B 380 "
           pdb=" CA  ARG B 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.01  -44.99     0      5.00e+00 4.00e-02 8.10e+01
  dihedral pdb=" CA  ARG A 663 "
           pdb=" C   ARG A 663 "
           pdb=" N   ASP A 664 "
           pdb=" CA  ASP A 664 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.72   26.28     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  ARG A 672 "
           pdb=" C   ARG A 672 "
           pdb=" N   PRO A 673 "
           pdb=" CA  PRO A 673 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.60   23.40     0      5.00e+00 4.00e-02 2.19e+01
  ... (remaining 7720 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.479: 1892
       0.479 -    0.957: 0
       0.957 -    1.436: 0
       1.436 -    1.914: 0
       1.914 -    2.393: 4
  Chirality restraints: 1896
  Sorted by residual:
  chirality pdb="FE4  SF4 A1401 "
            pdb=" S1  SF4 A1401 "
            pdb=" S2  SF4 A1401 "
            pdb=" S3  SF4 A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.55    8.16    2.39 2.00e-01 2.50e+01 1.43e+02
  chirality pdb="FE2  SF4 A1401 "
            pdb=" S1  SF4 A1401 "
            pdb=" S3  SF4 A1401 "
            pdb=" S4  SF4 A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.55    8.28    2.28 2.00e-01 2.50e+01 1.30e+02
  chirality pdb="FE1  SF4 A1401 "
            pdb=" S2  SF4 A1401 "
            pdb=" S3  SF4 A1401 "
            pdb=" S4  SF4 A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False    -10.55   -8.39   -2.17 2.00e-01 2.50e+01 1.17e+02
  ... (remaining 1893 not shown)

  Planarity restraints: 2200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  80 "   -0.022 2.00e-02 2.50e+03   4.30e-02 1.85e+01
        pdb=" C   THR A  80 "    0.074 2.00e-02 2.50e+03
        pdb=" O   THR A  80 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ASN A  81 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 863 "    0.021 2.00e-02 2.50e+03   4.27e-02 1.82e+01
        pdb=" C   ALA A 863 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   ALA A 863 "    0.028 2.00e-02 2.50e+03
        pdb=" N   LEU A 864 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 762 "   -0.021 2.00e-02 2.50e+03   4.18e-02 1.75e+01
        pdb=" C   VAL A 762 "    0.072 2.00e-02 2.50e+03
        pdb=" O   VAL A 762 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   CYS A 763 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 2197 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1541
        2.75 -     3.29: 12329
        3.29 -     3.83: 21221
        3.83 -     4.36: 24416
        4.36 -     4.90: 40289
  Nonbonded interactions: 99796
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 261 "
            pdb=" O   TRP B 284 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   LYS B 357 "
            pdb=" OG  SER B 360 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   TYR A 135 "
            pdb=" OH  TYR A 249 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   LEU D  73 "
            pdb=" OG  SER B   2 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OG1 THR A1068 "
            pdb=" O   THR A1103 "
     model   vdw
     2.296 3.040
  ... (remaining 99791 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=0.62 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:             1.410
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.350
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
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   0.182  12743  Z= 0.405
  Angle     :  1.557  24.254  17232  Z= 0.848
  Chirality :  0.129   2.393   1896
  Planarity :  0.009   0.088   2200
  Dihedral  : 14.137  89.031   4799
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.68 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  8.38 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.45 (0.19), residues: 1517
  helix: -0.89 (0.19), residues: 555
  sheet: -0.40 (0.30), residues: 248
  loop : -1.11 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP A  78 
 HIS   0.011   0.003   HIS A 915 
 PHE   0.058   0.004   PHE B 288 
 TYR   0.039   0.005   TYR A 245 
 ARG   0.027   0.002   ARG A 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16101 (  401)
  hydrogen bonds       : angle       6.40056 ( 1146)
  metal coordination   : bond        0.03913 (    4)
  metal coordination   : angle      11.95497 (   12)
  covalent geometry    : bond        0.00930 (12739)
  covalent geometry    : angle       1.52510 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 236
  time to evaluate  : 1.524 
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: symmetry clash
   revert: symmetry clash
REVERT: A   52 PHE cc_start: 0.8371 (m-80) cc_final: 0.7938 (m-10)
REVERT: A  121 PHE cc_start: 0.8616 (m-80) cc_final: 0.8094 (m-80)
REVERT: A  135 TYR cc_start: 0.8095 (t80) cc_final: 0.7468 (t80)
REVERT: A  148 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7894 (ptm160)
REVERT: A  151 ASP cc_start: 0.7662 (m-30) cc_final: 0.7442 (m-30)
REVERT: A  186 LYS cc_start: 0.8642 (tttp) cc_final: 0.8232 (tptt)
REVERT: A  314 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8353 (tpp)
REVERT: A  383 ASP cc_start: 0.7583 (m-30) cc_final: 0.6704 (m-30)
REVERT: A  453 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8337 (tp30)
REVERT: A  459 MET cc_start: 0.7464 (mtt) cc_final: 0.6782 (mtt)
REVERT: A  811 LYS cc_start: 0.8802 (mttp) cc_final: 0.8497 (mttt)
REVERT: A  827 LEU cc_start: 0.9539 (tt) cc_final: 0.9319 (tt)
REVERT: A  955 LEU cc_start: 0.8945 (mp) cc_final: 0.8693 (mp)
REVERT: A 1146 TYR cc_start: 0.8871 (m-80) cc_final: 0.8488 (m-10)
REVERT: D   78 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6722 (tm-30)
REVERT: D   81 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7671 (t)
REVERT: D  109 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8091 (mmmt)
REVERT: D  117 ASP cc_start: 0.8615 (t0) cc_final: 0.8332 (t0)
REVERT: B   16 LYS cc_start: 0.8870 (mttm) cc_final: 0.8595 (mmpt)
REVERT: B  232 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8652 (pt0)
REVERT: B  236 ASN cc_start: 0.8921 (m-40) cc_final: 0.8382 (p0)
REVERT: B  295 ASP cc_start: 0.7767 (p0) cc_final: 0.7547 (p0)
  outliers start: 26
  outliers final: 9
  residues processed: 257
  average time/residue: 0.2643
  time to fit residues: 96.3205
Evaluate side-chains
  175 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 164
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 77 optimal weight:    0.4980
   chunk 61 optimal weight:    5.9990
   chunk 119 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 138 optimal weight:    0.9980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A  83 HIS
A 444 GLN
A 450 ASN
A 490 HIS
A 638 HIS
A 671 ASN
A 973 ASN
A 999 GLN
** D  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  74 GLN
** D  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.085723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.069204 restraints weight = 63976.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.070904 restraints weight = 41017.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.071998 restraints weight = 30239.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3494
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12743  Z= 0.146
  Angle     :  0.787  33.506  17232  Z= 0.354
  Chirality :  0.045   0.201   1896
  Planarity :  0.005   0.053   2200
  Dihedral  :  5.558  69.512   1661
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.31 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -0.16 (0.21), residues: 1517
  helix:  0.68 (0.21), residues: 561
  sheet: -0.14 (0.32), residues: 243
  loop : -0.64 (0.23), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 841 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.019   0.002   PHE B 288 
 TYR   0.031   0.002   TYR A 412 
 ARG   0.009   0.001   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05197 (  401)
  hydrogen bonds       : angle       5.43495 ( 1146)
  metal coordination   : bond        0.00442 (    4)
  metal coordination   : angle      15.03590 (   12)
  covalent geometry    : bond        0.00300 (12739)
  covalent geometry    : angle       0.67992 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 203
  time to evaluate  : 1.419 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 PHE cc_start: 0.8621 (m-80) cc_final: 0.8177 (m-80)
REVERT: A  135 TYR cc_start: 0.8030 (t80) cc_final: 0.7395 (t80)
REVERT: A  186 LYS cc_start: 0.8447 (tttp) cc_final: 0.8111 (tptt)
REVERT: A  459 MET cc_start: 0.7755 (mtt) cc_final: 0.7059 (mtt)
REVERT: A  505 ASP cc_start: 0.8489 (m-30) cc_final: 0.8112 (m-30)
REVERT: A  517 GLU cc_start: 0.8656 (tt0) cc_final: 0.8339 (tm-30)
REVERT: A  521 MET cc_start: 0.9129 (mtt) cc_final: 0.7680 (tpp)
REVERT: A  811 LYS cc_start: 0.8633 (mttp) cc_final: 0.8395 (mttt)
REVERT: A  998 PHE cc_start: 0.8522 (t80) cc_final: 0.8309 (t80)
REVERT: A 1023 CYS cc_start: 0.7931 (t) cc_final: 0.7663 (t)
REVERT: A 1036 MET cc_start: 0.4713 (mmp) cc_final: 0.4343 (tpt)
REVERT: A 1165 GLN cc_start: 0.8114 (mp10) cc_final: 0.7555 (tm-30)
REVERT: D   30 MET cc_start: 0.7643 (mmm) cc_final: 0.7203 (mmm)
REVERT: D  109 LYS cc_start: 0.8358 (mmmt) cc_final: 0.8039 (mmmt)
REVERT: D  117 ASP cc_start: 0.8322 (t0) cc_final: 0.7927 (t0)
REVERT: D  119 MET cc_start: 0.8782 (mmp) cc_final: 0.8362 (mmp)
REVERT: B   16 LYS cc_start: 0.8901 (mttm) cc_final: 0.8678 (mmpt)
REVERT: B  232 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8765 (mt-10)
  outliers start: 2
  outliers final: 1
  residues processed: 203
  average time/residue: 0.2641
  time to fit residues: 77.6432
Evaluate side-chains
  149 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 1.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 17 optimal weight:    0.9990
   chunk 141 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0070
   chunk 151 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 13 optimal weight:    0.6980
   chunk 138 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   overall best weight:    0.5540

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 627 ASN
A1033 HIS
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  88 GLN
** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.085811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.069506 restraints weight = 64511.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.071170 restraints weight = 41687.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.072208 restraints weight = 30972.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  12743  Z= 0.112
  Angle     :  0.684  26.681  17232  Z= 0.306
  Chirality :  0.043   0.173   1896
  Planarity :  0.004   0.053   2200
  Dihedral  :  5.033  63.345   1661
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.96 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.21), residues: 1517
  helix:  0.92 (0.21), residues: 565
  sheet: -0.15 (0.32), residues: 255
  loop : -0.46 (0.24), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 284 
 HIS   0.003   0.001   HIS A 490 
 PHE   0.016   0.001   PHE A1003 
 TYR   0.023   0.001   TYR A 412 
 ARG   0.007   0.000   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04367 (  401)
  hydrogen bonds       : angle       5.11835 ( 1146)
  metal coordination   : bond        0.00228 (    4)
  metal coordination   : angle      12.71368 (   12)
  covalent geometry    : bond        0.00233 (12739)
  covalent geometry    : angle       0.59671 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 1.474 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8805 (m-30) cc_final: 0.8392 (m-30)
REVERT: A  135 TYR cc_start: 0.7928 (t80) cc_final: 0.7363 (t80)
REVERT: A  186 LYS cc_start: 0.8357 (tttp) cc_final: 0.8093 (tptt)
REVERT: A  415 SER cc_start: 0.8588 (p) cc_final: 0.7807 (p)
REVERT: A  452 ILE cc_start: 0.7477 (tp) cc_final: 0.7093 (pt)
REVERT: A  459 MET cc_start: 0.7714 (mtt) cc_final: 0.7192 (mtt)
REVERT: A  521 MET cc_start: 0.9113 (mtt) cc_final: 0.8497 (mtt)
REVERT: A  835 MET cc_start: 0.8884 (mpp) cc_final: 0.8617 (mpp)
REVERT: A 1036 MET cc_start: 0.4720 (mmp) cc_final: 0.4430 (tpt)
REVERT: A 1165 GLN cc_start: 0.7972 (mp10) cc_final: 0.7588 (tm-30)
REVERT: D  101 MET cc_start: 0.8589 (tpp) cc_final: 0.8381 (tpp)
REVERT: D  117 ASP cc_start: 0.8103 (t0) cc_final: 0.7884 (t0)
REVERT: D  119 MET cc_start: 0.8666 (mmp) cc_final: 0.7967 (mmm)
REVERT: B   52 CYS cc_start: 0.7694 (p) cc_final: 0.7490 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 191
  average time/residue: 0.2301
  time to fit residues: 65.7353
Evaluate side-chains
  151 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0470
   chunk 11 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0370
   chunk 135 optimal weight:    5.9990
   chunk 125 optimal weight:    3.9990
   chunk 127 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    2.4162

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 HIS
A 444 GLN
A 764 GLN
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 212 HIS
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.082650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.066611 restraints weight = 65106.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.068159 restraints weight = 42757.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.069179 restraints weight = 32070.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12743  Z= 0.175
  Angle     :  0.760  28.097  17232  Z= 0.330
  Chirality :  0.044   0.161   1896
  Planarity :  0.005   0.046   2200
  Dihedral  :  5.062  62.524   1661
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -0.08 (0.21), residues: 1517
  helix:  0.81 (0.21), residues: 565
  sheet: -0.32 (0.32), residues: 252
  loop : -0.58 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 284 
 HIS   0.005   0.001   HIS A 365 
 PHE   0.022   0.002   PHE A 777 
 TYR   0.024   0.002   TYR A 412 
 ARG   0.008   0.001   ARG B 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04321 (  401)
  hydrogen bonds       : angle       5.13997 ( 1146)
  metal coordination   : bond        0.01000 (    4)
  metal coordination   : angle      15.63450 (   12)
  covalent geometry    : bond        0.00379 (12739)
  covalent geometry    : angle       0.63851 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.401 
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: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8852 (m-30) cc_final: 0.8494 (m-30)
REVERT: A  135 TYR cc_start: 0.8139 (t80) cc_final: 0.7427 (t80)
REVERT: A  186 LYS cc_start: 0.8603 (tttp) cc_final: 0.8228 (tptt)
REVERT: A  415 SER cc_start: 0.8618 (p) cc_final: 0.7879 (p)
REVERT: A  459 MET cc_start: 0.7735 (mtt) cc_final: 0.7256 (mtt)
REVERT: A  517 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7849 (tm-30)
REVERT: A  531 LEU cc_start: 0.8741 (mp) cc_final: 0.8268 (mm)
REVERT: A  811 LYS cc_start: 0.8734 (mttp) cc_final: 0.8360 (mttt)
REVERT: A  953 MET cc_start: 0.8332 (tpt) cc_final: 0.8111 (tpp)
REVERT: A 1036 MET cc_start: 0.4950 (mmp) cc_final: 0.4681 (tpt)
REVERT: A 1165 GLN cc_start: 0.8044 (mp10) cc_final: 0.7542 (tm-30)
REVERT: D  119 MET cc_start: 0.8621 (mmp) cc_final: 0.8392 (mmp)
REVERT: B  232 GLU cc_start: 0.8979 (pt0) cc_final: 0.8672 (pp20)
REVERT: B  356 MET cc_start: 0.7362 (ptm) cc_final: 0.7087 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2505
  time to fit residues: 67.5162
Evaluate side-chains
  139 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 136 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 100 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 131 optimal weight:    3.9990
   chunk 135 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 147 optimal weight:    0.8980
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 HIS
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 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 = 0.3721 r_free = 0.3721 target = 0.081907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.066034 restraints weight = 63746.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.067590 restraints weight = 41428.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.068660 restraints weight = 30842.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12743  Z= 0.175
  Angle     :  0.759  29.627  17232  Z= 0.324
  Chirality :  0.044   0.192   1896
  Planarity :  0.004   0.048   2200
  Dihedral  :  5.021  60.173   1661
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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 (0.21), residues: 1517
  helix:  0.79 (0.21), residues: 566
  sheet: -0.33 (0.32), residues: 262
  loop : -0.62 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 284 
 HIS   0.004   0.001   HIS A 365 
 PHE   0.020   0.002   PHE B 288 
 TYR   0.022   0.002   TYR A 416 
 ARG   0.008   0.001   ARG A 806 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04210 (  401)
  hydrogen bonds       : angle       5.06574 ( 1146)
  metal coordination   : bond        0.01121 (    4)
  metal coordination   : angle      16.00495 (   12)
  covalent geometry    : bond        0.00379 (12739)
  covalent geometry    : angle       0.63039 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.814 
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: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8801 (m-30) cc_final: 0.8566 (m-30)
REVERT: A  135 TYR cc_start: 0.8153 (t80) cc_final: 0.7414 (t80)
REVERT: A  186 LYS cc_start: 0.8718 (tttp) cc_final: 0.8063 (tptt)
REVERT: A  459 MET cc_start: 0.7648 (mtt) cc_final: 0.7146 (mtt)
REVERT: A  517 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7582 (tm-30)
REVERT: A  811 LYS cc_start: 0.8736 (mttp) cc_final: 0.8397 (mttt)
REVERT: A 1165 GLN cc_start: 0.8088 (mp10) cc_final: 0.7627 (tm-30)
REVERT: D  119 MET cc_start: 0.8567 (mmp) cc_final: 0.8050 (mmm)
REVERT: B  232 GLU cc_start: 0.8968 (pt0) cc_final: 0.8653 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.3018
  time to fit residues: 78.7333
Evaluate side-chains
  141 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 145 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 110 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 133 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 134 optimal weight:    4.9990
   chunk 139 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0270
   overall best weight:    1.6046

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 197 ASN
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 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 = 0.3728 r_free = 0.3728 target = 0.082260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.066409 restraints weight = 64224.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.068007 restraints weight = 41797.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.069057 restraints weight = 31066.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12743  Z= 0.133
  Angle     :  0.716  28.083  17232  Z= 0.304
  Chirality :  0.043   0.171   1896
  Planarity :  0.004   0.049   2200
  Dihedral  :  4.889  58.301   1661
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.95 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -0.03 (0.21), residues: 1517
  helix:  0.86 (0.21), residues: 568
  sheet: -0.24 (0.32), residues: 263
  loop : -0.59 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 284 
 HIS   0.005   0.001   HIS A 365 
 PHE   0.013   0.001   PHE A 998 
 TYR   0.021   0.002   TYR A 416 
 ARG   0.004   0.000   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  401)
  hydrogen bonds       : angle       5.00987 ( 1146)
  metal coordination   : bond        0.00723 (    4)
  metal coordination   : angle      15.06744 (   12)
  covalent geometry    : bond        0.00289 (12739)
  covalent geometry    : angle       0.59573 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 1.573 
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  135 TYR cc_start: 0.8076 (t80) cc_final: 0.7261 (t80)
REVERT: A  186 LYS cc_start: 0.8634 (tttp) cc_final: 0.8004 (tptt)
REVERT: A  459 MET cc_start: 0.7618 (mtt) cc_final: 0.7091 (mtt)
REVERT: A  517 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7746 (tm-30)
REVERT: A  521 MET cc_start: 0.9138 (mmt) cc_final: 0.8836 (mmm)
REVERT: A  567 ARG cc_start: 0.6202 (mtm180) cc_final: 0.5744 (mtm180)
REVERT: A  953 MET cc_start: 0.8534 (tpp) cc_final: 0.7722 (tpp)
REVERT: A 1165 GLN cc_start: 0.7949 (mp10) cc_final: 0.7541 (tm-30)
REVERT: B   52 CYS cc_start: 0.7919 (p) cc_final: 0.7599 (t)
REVERT: B  232 GLU cc_start: 0.8899 (pt0) cc_final: 0.8673 (pp20)
REVERT: B  356 MET cc_start: 0.7403 (ptm) cc_final: 0.7115 (ptp)
  outliers start: 1
  outliers final: 1
  residues processed: 178
  average time/residue: 0.3406
  time to fit residues: 91.3720
Evaluate side-chains
  141 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 2.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 122 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0010
   chunk 32 optimal weight:    0.7980
   chunk 117 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 139 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    2.1592

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 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 = 0.3714 r_free = 0.3714 target = 0.081423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.065551 restraints weight = 65906.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.067127 restraints weight = 42576.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.068158 restraints weight = 31522.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12743  Z= 0.161
  Angle     :  0.747  28.605  17232  Z= 0.321
  Chirality :  0.044   0.174   1896
  Planarity :  0.004   0.050   2200
  Dihedral  :  4.900  53.069   1661
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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 (0.21), residues: 1517
  helix:  0.81 (0.21), residues: 572
  sheet: -0.38 (0.32), residues: 264
  loop : -0.53 (0.24), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP B 284 
 HIS   0.004   0.001   HIS A 365 
 PHE   0.031   0.002   PHE A 594 
 TYR   0.019   0.002   TYR A 416 
 ARG   0.004   0.000   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04064 (  401)
  hydrogen bonds       : angle       5.03778 ( 1146)
  metal coordination   : bond        0.00856 (    4)
  metal coordination   : angle      15.61613 (   12)
  covalent geometry    : bond        0.00349 (12739)
  covalent geometry    : angle       0.62282 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8832 (m-30) cc_final: 0.8568 (m-30)
REVERT: A  135 TYR cc_start: 0.8082 (t80) cc_final: 0.7313 (t80)
REVERT: A  186 LYS cc_start: 0.8728 (tttp) cc_final: 0.8082 (tptt)
REVERT: A  459 MET cc_start: 0.7673 (mtt) cc_final: 0.7165 (mtt)
REVERT: A  517 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7787 (tm-30)
REVERT: A  567 ARG cc_start: 0.6247 (mtm180) cc_final: 0.5800 (mtm180)
REVERT: A  657 ASP cc_start: 0.7801 (p0) cc_final: 0.7478 (p0)
REVERT: A  953 MET cc_start: 0.8624 (tpp) cc_final: 0.7862 (tpp)
REVERT: A 1165 GLN cc_start: 0.8051 (mp10) cc_final: 0.7612 (tm-30)
REVERT: D   45 PHE cc_start: 0.7652 (m-10) cc_final: 0.7436 (m-10)
REVERT: D   90 LEU cc_start: 0.8993 (mt) cc_final: 0.8772 (mt)
REVERT: B   52 CYS cc_start: 0.7929 (p) cc_final: 0.7678 (t)
REVERT: B  232 GLU cc_start: 0.8958 (pt0) cc_final: 0.8685 (pp20)
REVERT: B  323 MET cc_start: 0.8374 (mmm) cc_final: 0.8056 (mmm)
REVERT: B  356 MET cc_start: 0.7263 (ptm) cc_final: 0.7007 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.3427
  time to fit residues: 89.1320
Evaluate side-chains
  137 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 38 optimal weight:    0.0270
   chunk 70 optimal weight:    4.9990
   chunk 99 optimal weight:    0.0370
   chunk 121 optimal weight:    9.9990
   chunk 102 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 10 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 147 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   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  83 HIS
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 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 = 0.3752 r_free = 0.3752 target = 0.083320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.067361 restraints weight = 64424.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.068991 restraints weight = 41888.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.070095 restraints weight = 31006.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12743  Z= 0.106
  Angle     :  0.691  25.822  17232  Z= 0.298
  Chirality :  0.043   0.173   1896
  Planarity :  0.004   0.049   2200
  Dihedral  :  4.696  49.791   1661
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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:  0.08 (0.22), residues: 1517
  helix:  0.84 (0.21), residues: 567
  sheet: -0.21 (0.33), residues: 258
  loop : -0.40 (0.24), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 284 
 HIS   0.003   0.001   HIS A 180 
 PHE   0.034   0.001   PHE A 777 
 TYR   0.015   0.001   TYR A 249 
 ARG   0.002   0.000   ARG A 780 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03734 (  401)
  hydrogen bonds       : angle       4.95999 ( 1146)
  metal coordination   : bond        0.00320 (    4)
  metal coordination   : angle      13.51790 (   12)
  covalent geometry    : bond        0.00226 (12739)
  covalent geometry    : angle       0.59163 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 4.738 
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   47 ASP cc_start: 0.8676 (m-30) cc_final: 0.8427 (m-30)
REVERT: A  135 TYR cc_start: 0.8002 (t80) cc_final: 0.7369 (t80)
REVERT: A  173 GLU cc_start: 0.7843 (mp0) cc_final: 0.7200 (mp0)
REVERT: A  186 LYS cc_start: 0.8662 (tttp) cc_final: 0.8056 (tptt)
REVERT: A  459 MET cc_start: 0.7544 (mtt) cc_final: 0.7053 (mtt)
REVERT: A  483 TYR cc_start: 0.8539 (m-80) cc_final: 0.8332 (m-10)
REVERT: A  517 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7922 (tm-30)
REVERT: A  528 ASN cc_start: 0.8829 (t0) cc_final: 0.8260 (t0)
REVERT: A  637 TYR cc_start: 0.7752 (m-10) cc_final: 0.7361 (m-80)
REVERT: A  657 ASP cc_start: 0.7791 (p0) cc_final: 0.7413 (p0)
REVERT: A  953 MET cc_start: 0.8510 (tpp) cc_final: 0.7764 (tpp)
REVERT: A 1083 LYS cc_start: 0.6559 (tppt) cc_final: 0.5716 (ttmt)
REVERT: A 1165 GLN cc_start: 0.7840 (mp10) cc_final: 0.7548 (tm-30)
REVERT: D  119 MET cc_start: 0.8594 (mmp) cc_final: 0.7746 (mmm)
REVERT: B   52 CYS cc_start: 0.7896 (p) cc_final: 0.7680 (t)
REVERT: B  323 MET cc_start: 0.8370 (mmm) cc_final: 0.8035 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.3994
  time to fit residues: 117.2196
Evaluate side-chains
  142 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 144 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 76 optimal weight:    9.9990
   chunk 94 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0050
   chunk 5 optimal weight:    6.9990
   chunk 126 optimal weight:    5.9990
   overall best weight:    1.5596

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 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 = 0.3727 r_free = 0.3727 target = 0.081980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.066273 restraints weight = 64409.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.067845 restraints weight = 41836.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.068824 restraints weight = 31067.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  12743  Z= 0.133
  Angle     :  0.720  26.833  17232  Z= 0.312
  Chirality :  0.043   0.171   1896
  Planarity :  0.004   0.049   2200
  Dihedral  :  4.682  43.879   1661
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.22), residues: 1517
  helix:  0.87 (0.21), residues: 572
  sheet: -0.22 (0.34), residues: 254
  loop : -0.39 (0.24), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 284 
 HIS   0.003   0.001   HIS A1033 
 PHE   0.024   0.001   PHE A 193 
 TYR   0.025   0.001   TYR A 416 
 ARG   0.005   0.000   ARG A 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  401)
  hydrogen bonds       : angle       4.94959 ( 1146)
  metal coordination   : bond        0.00578 (    4)
  metal coordination   : angle      14.25279 (   12)
  covalent geometry    : bond        0.00295 (12739)
  covalent geometry    : angle       0.61392 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8616 (m-30) cc_final: 0.8410 (m-30)
REVERT: A  121 PHE cc_start: 0.8680 (m-80) cc_final: 0.8342 (m-80)
REVERT: A  135 TYR cc_start: 0.8091 (t80) cc_final: 0.7326 (t80)
REVERT: A  186 LYS cc_start: 0.8775 (tttp) cc_final: 0.8200 (tptt)
REVERT: A  459 MET cc_start: 0.7608 (mtt) cc_final: 0.7110 (mtt)
REVERT: A  515 LEU cc_start: 0.9643 (mm) cc_final: 0.9442 (mt)
REVERT: A  517 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8123 (tm-30)
REVERT: A  637 TYR cc_start: 0.7847 (m-10) cc_final: 0.7447 (m-80)
REVERT: A  657 ASP cc_start: 0.7890 (p0) cc_final: 0.7453 (p0)
REVERT: A  860 MET cc_start: 0.8396 (tmm) cc_final: 0.8078 (tmm)
REVERT: A  953 MET cc_start: 0.8622 (tpp) cc_final: 0.7971 (tpp)
REVERT: A 1023 CYS cc_start: 0.8076 (t) cc_final: 0.7811 (t)
REVERT: A 1165 GLN cc_start: 0.7974 (mp10) cc_final: 0.7655 (tm-30)
REVERT: D   90 LEU cc_start: 0.8928 (mt) cc_final: 0.8701 (mt)
REVERT: B   52 CYS cc_start: 0.8009 (p) cc_final: 0.7704 (t)
REVERT: B  323 MET cc_start: 0.8324 (mmm) cc_final: 0.8013 (mmm)
REVERT: B  356 MET cc_start: 0.7269 (ptm) cc_final: 0.7062 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.2401
  time to fit residues: 62.5212
Evaluate side-chains
  138 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 118 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 107 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 132 optimal weight:    0.6980
   chunk 105 optimal weight:    6.9990
   chunk 106 optimal weight:    0.3980
   chunk 76 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.083005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.067084 restraints weight = 64975.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.068698 restraints weight = 42026.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.069753 restraints weight = 31178.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12743  Z= 0.115
  Angle     :  0.710  25.790  17232  Z= 0.310
  Chirality :  0.044   0.203   1896
  Planarity :  0.004   0.049   2200
  Dihedral  :  4.627  41.635   1661
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.22), residues: 1517
  helix:  0.89 (0.21), residues: 567
  sheet: -0.25 (0.34), residues: 254
  loop : -0.38 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP B 284 
 HIS   0.003   0.001   HIS A 365 
 PHE   0.019   0.001   PHE A 777 
 TYR   0.024   0.001   TYR A 416 
 ARG   0.009   0.000   ARG A1173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03744 (  401)
  hydrogen bonds       : angle       4.92265 ( 1146)
  metal coordination   : bond        0.00367 (    4)
  metal coordination   : angle      13.62741 (   12)
  covalent geometry    : bond        0.00253 (12739)
  covalent geometry    : angle       0.61240 (17220)

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

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

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3034 Ramachandran restraints generated.
    1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.716 
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  121 PHE cc_start: 0.8624 (m-80) cc_final: 0.8421 (m-80)
REVERT: A  135 TYR cc_start: 0.8020 (t80) cc_final: 0.7450 (t80)
REVERT: A  186 LYS cc_start: 0.8770 (tttp) cc_final: 0.8161 (tptt)
REVERT: A  459 MET cc_start: 0.7624 (mtt) cc_final: 0.7137 (mtt)
REVERT: A  483 TYR cc_start: 0.8567 (m-80) cc_final: 0.8348 (m-10)
REVERT: A  517 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7704 (tm-30)
REVERT: A  528 ASN cc_start: 0.8874 (t0) cc_final: 0.8372 (t0)
REVERT: A  567 ARG cc_start: 0.6395 (mtm180) cc_final: 0.5881 (mtm180)
REVERT: A  637 TYR cc_start: 0.7867 (m-10) cc_final: 0.7448 (m-80)
REVERT: A  657 ASP cc_start: 0.7820 (p0) cc_final: 0.7381 (p0)
REVERT: A  953 MET cc_start: 0.8611 (tpp) cc_final: 0.7962 (tpp)
REVERT: A 1083 LYS cc_start: 0.6494 (tppt) cc_final: 0.5631 (ttpt)
REVERT: A 1165 GLN cc_start: 0.7878 (mp10) cc_final: 0.7614 (tm-30)
REVERT: D   84 VAL cc_start: 0.7590 (t) cc_final: 0.7375 (t)
REVERT: B   52 CYS cc_start: 0.7892 (p) cc_final: 0.7683 (t)
REVERT: B  323 MET cc_start: 0.8319 (mmm) cc_final: 0.7991 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.2198
  time to fit residues: 58.4040
Evaluate side-chains
  141 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 120 optimal weight:    0.6980
   chunk 90 optimal weight:    7.9990
   chunk 128 optimal weight:    3.9990
   chunk 118 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 95 optimal weight:    5.9990
   chunk 127 optimal weight:    3.9990
   chunk 119 optimal weight:    0.0770
   chunk 56 optimal weight:    0.7980
   chunk 133 optimal weight:    4.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.083644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.067615 restraints weight = 64832.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.069203 restraints weight = 42324.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.070214 restraints weight = 31553.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082  12743  Z= 0.115
  Angle     :  0.693  24.690  17232  Z= 0.306
  Chirality :  0.043   0.173   1896
  Planarity :  0.004   0.054   2200
  Dihedral  :  4.509  40.370   1661
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.22), residues: 1517
  helix:  0.86 (0.22), residues: 566
  sheet: -0.21 (0.34), residues: 254
  loop : -0.38 (0.24), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 260 
 HIS   0.010   0.001   HIS A 490 
 PHE   0.019   0.001   PHE D  59 
 TYR   0.020   0.001   TYR B 261 
 ARG   0.007   0.000   ARG A1173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  401)
  hydrogen bonds       : angle       4.96803 ( 1146)
  metal coordination   : bond        0.00267 (    4)
  metal coordination   : angle      12.91438 (   12)
  covalent geometry    : bond        0.00255 (12739)
  covalent geometry    : angle       0.60349 (17220)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4408.93 seconds
wall clock time: 81 minutes 9.12 seconds (4869.12 seconds total)