Starting phenix.real_space_refine
on Thu Feb 13 01:25:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d9u_30621/02_2025/7d9u_30621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d9u_30621/02_2025/7d9u_30621.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d9u_30621/02_2025/7d9u_30621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d9u_30621/02_2025/7d9u_30621.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d9u_30621/02_2025/7d9u_30621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d9u_30621/02_2025/7d9u_30621.cif"
  }
  resolution = 3.8
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      2      5.21       5
     S      56      5.16       5
     C    5264      2.51       5
     N    1389      2.21       5
     O    1476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8190
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3742
          Classifications: {'peptide': 506}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 23, 'TRANS': 482}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 261
          Unresolved non-hydrogen angles: 319
          Unresolved non-hydrogen dihedrals: 216
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 162
    Chain: "B"
      Number of atoms: 4372
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 569, 4368
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 148
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 138
      Conformer: "B"
        Number of residues, atoms: 569, 4368
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 148
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 138
          bond proxies already assigned to first conformer: 4452
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {' MG': 2, 'G2P': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'Z90': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LEU A 254 " occ=0.92
      ... (3 atoms not shown)
      pdb=" CB  LEU A 254 " occ=0.92
  Time building chain proxies: 7.24, per 1000 atoms: 0.88
  Number of scatterers: 8190
  At special positions: 0
  Unit cell: (99.275, 137.94, 137.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      56     16.00
     P       3     15.00
     Mg      2     11.99
     O    1476      8.00
     N    1389      7.00
     C    5264      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: 2.29
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 11 sheets defined
      49.6% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 83
    Processing helix  chain 'A' and resid 85 through 101
    Processing helix  chain 'A' and resid 115 through 126
    Processing helix  chain 'A' and resid 128 through 146
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 3.892A  pdb=" N   PHE A 166 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   SER A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   THR A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 226
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'A' and resid 302 through 309
    Processing helix  chain 'A' and resid 334 through 341
    Processing helix  chain 'A' and resid 399 through 403
    Processing helix  chain 'A' and resid 408 through 458
      removed outlier: 3.853A  pdb=" N   VAL A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 468
      removed outlier: 4.240A  pdb=" N   GLN A 468 " --> pdb=" O   GLN A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 497
      removed outlier: 3.637A  pdb=" N   ILE A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 519
      removed outlier: 3.699A  pdb=" N   GLU A 519 " --> pdb=" O   GLN A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 561
    Processing helix  chain 'A' and resid 598 through 610
      removed outlier: 3.884A  pdb=" N   THR A 602 " --> pdb=" O   GLY A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 627
    Processing helix  chain 'B' and resid 2 through 29
      removed outlier: 4.084A  pdb=" N   ASN B   6 " --> pdb=" O   TYR B   2 " (cutoff:3.500A)
      Proline residue:  B  19  - end of helix
      removed outlier: 3.820A  pdb=" N   TRP B  22 " --> pdb=" O   GLY B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 59
      removed outlier: 3.803A  pdb=" N   THR B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 82
      removed outlier: 3.699A  pdb=" N   ILE B  66 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 90
      removed outlier: 3.850A  pdb=" N   LEU B  87 " --> pdb=" O   TYR B  83 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU B  90 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 112
      removed outlier: 4.597A  pdb=" N   ASP B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   ALA B 103 " --> pdb=" O   GLN B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 158
      removed outlier: 3.774A  pdb=" N   ILE B 147 " --> pdb=" O   GLN B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 235 through 240
    Processing helix  chain 'B' and resid 249 through 253
      removed outlier: 3.865A  pdb=" N   VAL B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 253'
    Processing helix  chain 'B' and resid 264 through 271
    Processing helix  chain 'B' and resid 282 through 285
      removed outlier: 4.365A  pdb=" N   LEU B 285 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 282 through 285'
    Processing helix  chain 'B' and resid 329 through 335
      removed outlier: 3.668A  pdb=" N   LEU B 333 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 348 through 398
      removed outlier: 4.393A  pdb=" N   LEU B 354 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 408
      removed outlier: 4.247A  pdb=" N   HIS B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 437
    Processing helix  chain 'B' and resid 443 through 461
    Processing helix  chain 'B' and resid 491 through 507
      removed outlier: 3.848A  pdb=" N   SER B 495 " --> pdb=" O   HIS B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 557
      removed outlier: 3.710A  pdb=" N   ASN B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 574
      removed outlier: 3.917A  pdb=" N   SER B 574 " --> pdb=" O   ARG B 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 234
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300
      removed outlier: 6.405A  pdb=" N   MET A 291 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A 290 " --> pdb=" O   PHE A 381 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE A 292 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLY A 368 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 525
      removed outlier: 4.296A  pdb=" N   CYS A 533 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR A 481 " --> pdb=" O   GLY A 536 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE A 484 " --> pdb=" O   GLY A 576 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 583 through 585
    Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 124
      removed outlier: 3.617A  pdb=" N   ARG B 121 " --> pdb=" O   HIS B 134 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 162 through 164
      removed outlier: 3.941A  pdb=" N   ASP B 163 " --> pdb=" O   GLU B 182 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLU B 182 " --> pdb=" O   ASP B 163 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 231
      removed outlier: 3.658A  pdb=" N   PHE B 223 " --> pdb=" O   ILE B 319 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE B 319 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   VAL B 277 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 415 through 417
      removed outlier: 3.686A  pdb=" N   GLY B 531 " --> pdb=" O   CYS B 541 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   CYS B 541 " --> pdb=" O   GLY B 531 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 478 through 479
      removed outlier: 3.591A  pdb=" N   ILE B 422 " --> pdb=" O   HIS B 524 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   HIS B 524 " --> pdb=" O   ILE B 422 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   ASN B 563 " --> pdb=" O   ILE B 519 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   SER B 565 " --> pdb=" O   ILE B 521 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ILE B 523 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   MET B 599 " --> pdb=" O   PRO B 589 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL B 601 " --> pdb=" O   ARG B 587 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 469 through 470
    Processing sheet with id=AB2, first strand: chain 'B' and resid 511 through 512

    441 hydrogen bonds defined for protein.
    1260 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: 2.48

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2635
        1.34 -     1.46: 1766
        1.46 -     1.58: 3858
        1.58 -     1.69: 5
        1.69 -     1.81: 86
  Bond restraints: 8350
  Sorted by residual:
  bond pdb=" O3B G2P A1001 "
       pdb=" PG  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.716  1.606  0.110 2.00e-02 2.50e+03 3.02e+01
  bond pdb=" O1A G2P A1001 "
       pdb=" PA  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.507  1.608 -0.101 2.00e-02 2.50e+03 2.57e+01
  bond pdb=" O1B G2P A1001 "
       pdb=" PB  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.510  1.608 -0.098 2.00e-02 2.50e+03 2.43e+01
  bond pdb=" C4  G2P A1001 "
       pdb=" C5  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.384  1.467 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" CBN Z90 B 701 "
       pdb=" CBO Z90 B 701 "
    ideal  model  delta    sigma   weight residual
    1.405  1.480 -0.075 2.00e-02 2.50e+03 1.39e+01
  ... (remaining 8345 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 11226
        2.26 -     4.52: 94
        4.52 -     6.77: 12
        6.77 -     9.03: 7
        9.03 -    11.29: 4
  Bond angle restraints: 11343
  Sorted by residual:
  angle pdb=" C3A G2P A1001 "
        pdb=" PB  G2P A1001 "
        pdb=" O3B G2P A1001 "
      ideal   model   delta    sigma   weight residual
      99.71  111.00  -11.29 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" PA  G2P A1001 "
        pdb=" C3A G2P A1001 "
        pdb=" PB  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     120.83  110.32   10.51 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" C3A G2P A1001 "
        pdb=" PA  G2P A1001 "
        pdb=" O5' G2P A1001 "
      ideal   model   delta    sigma   weight residual
      99.14  109.41  -10.27 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" C5  G2P A1001 "
        pdb=" C4  G2P A1001 "
        pdb=" N3  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     128.08  118.68    9.40 3.00e+00 1.11e-01 9.81e+00
  angle pdb=" N3  G2P A1001 "
        pdb=" C4  G2P A1001 "
        pdb=" N9  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     126.73  134.95   -8.22 3.00e+00 1.11e-01 7.51e+00
  ... (remaining 11338 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.93: 4833
       24.93 -    49.86: 153
       49.86 -    74.80: 11
       74.80 -    99.73: 2
       99.73 -   124.66: 2
  Dihedral angle restraints: 5001
    sinusoidal: 1878
      harmonic: 3123
  Sorted by residual:
  dihedral pdb=" CAX Z90 B 701 "
           pdb=" CAV Z90 B 701 "
           pdb=" CAW Z90 B 701 "
           pdb=" CBB Z90 B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.41  -55.93 -124.66     1      3.00e+01 1.11e-03 1.67e+01
  dihedral pdb=" CAW Z90 B 701 "
           pdb=" CBB Z90 B 701 "
           pdb=" NBP Z90 B 701 "
           pdb=" CBC Z90 B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -158.43  -36.24 -122.19     1      3.00e+01 1.11e-03 1.63e+01
  dihedral pdb=" CA  LEU B 338 "
           pdb=" C   LEU B 338 "
           pdb=" N   TYR B 339 "
           pdb=" CA  TYR B 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.21   15.79     0      5.00e+00 4.00e-02 9.97e+00
  ... (remaining 4998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 875
       0.032 -    0.063: 316
       0.063 -    0.095: 101
       0.095 -    0.127: 46
       0.127 -    0.158: 4
  Chirality restraints: 1342
  Sorted by residual:
  chirality pdb=" C1' G2P A1001 "
            pdb=" C2' G2P A1001 "
            pdb=" N9  G2P A1001 "
            pdb=" O4' G2P A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.52   -0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  PRO B 210 "
            pdb=" N   PRO B 210 "
            pdb=" C   PRO B 210 "
            pdb=" CB  PRO B 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" C2' G2P A1001 "
            pdb=" C1' G2P A1001 "
            pdb=" C3' G2P A1001 "
            pdb=" O2' G2P A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.62    0.14 2.00e-01 2.50e+01 5.01e-01
  ... (remaining 1339 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 565 "   -0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO A 566 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 566 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 566 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 485 "    0.005 2.00e-02 2.50e+03   1.09e-02 1.19e+00
        pdb=" C   SER A 485 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   SER A 485 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ASP A 486 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 642 "    0.018 5.00e-02 4.00e+02   2.72e-02 1.19e+00
        pdb=" N   PRO A 643 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 643 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 643 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 499
        2.73 -     3.27: 8569
        3.27 -     3.81: 13433
        3.81 -     4.36: 15179
        4.36 -     4.90: 26681
  Nonbonded interactions: 64361
  Sorted by model distance:
  nonbonded pdb=" O1A G2P A1001 "
            pdb=" O3B G2P A1001 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OG  SER B 280 "
            pdb=" O   CYS B 303 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   LEU A 520 "
            pdb=" NE2 GLN A 548 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OD1 ASN B   6 "
            pdb=" OG1 THR B  48 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OD1 ASP A 486 "
            pdb="MG    MG A1003 "
     model   vdw
     2.245 2.170
  ... (remaining 64356 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=0.30 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:             1.000
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     24.270
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
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      :  0.004   0.110   8350  Z= 0.281
  Angle     :  0.592  11.289  11343  Z= 0.292
  Chirality :  0.040   0.158   1342
  Planarity :  0.003   0.034   1431
  Dihedral  : 12.325 124.661   2975
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.43 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.72 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.24), residues: 1049
  helix: -0.18 (0.21), residues: 476
  sheet: -2.02 (0.35), residues: 189
  loop : -2.55 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  22 
 HIS   0.002   0.001   HIS A 539 
 PHE   0.012   0.001   PHE A 607 
 TYR   0.011   0.001   TYR B   2 
 ARG   0.001   0.000   ARG A  88 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8286 (pp20) cc_final: 0.7546 (pp20)
REVERT: A  255 TYR cc_start: 0.7250 (m-80) cc_final: 0.6734 (m-10)
REVERT: A  399 TYR cc_start: 0.8432 (m-80) cc_final: 0.7619 (m-10)
REVERT: A  443 LEU cc_start: 0.8824 (tp) cc_final: 0.8605 (tp)
REVERT: A  444 GLU cc_start: 0.8808 (tp30) cc_final: 0.8364 (tm-30)
REVERT: A  452 ASP cc_start: 0.8567 (t0) cc_final: 0.8353 (t0)
REVERT: A  583 PHE cc_start: 0.8736 (m-80) cc_final: 0.8223 (m-80)
REVERT: A  591 MET cc_start: 0.8850 (tpp) cc_final: 0.8368 (tpt)
REVERT: A  597 PHE cc_start: 0.8246 (m-80) cc_final: 0.8021 (m-80)
REVERT: B   73 MET cc_start: 0.8435 (tpp) cc_final: 0.8040 (tpt)
REVERT: B  284 LEU cc_start: 0.9155 (mt) cc_final: 0.8890 (mp)
REVERT: B  479 TYR cc_start: 0.8549 (t80) cc_final: 0.8179 (t80)
REVERT: B  480 MET cc_start: 0.8763 (ttt) cc_final: 0.8563 (ttt)
REVERT: B  563 ASN cc_start: 0.7915 (p0) cc_final: 0.7706 (p0)
REVERT: B  569 TYR cc_start: 0.8868 (t80) cc_final: 0.8572 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1971
  time to fit residues: 39.9114
Evaluate side-chains
  97 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
A 303 ASN
A 422 GLN
B 242 GLN
B 266 HIS
B 346 HIS
B 408 HIS
B 437 HIS
B 451 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.083803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.068134 restraints weight = 31761.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.070694 restraints weight = 15373.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.072393 restraints weight = 9429.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8350  Z= 0.196
  Angle     :  0.566   8.623  11343  Z= 0.289
  Chirality :  0.042   0.142   1342
  Planarity :  0.004   0.041   1431
  Dihedral  :  8.815 134.951   1189
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 12.63 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.26), residues: 1049
  helix:  0.76 (0.23), residues: 486
  sheet: -1.74 (0.36), residues: 186
  loop : -2.09 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.005   TRP B 602 
 HIS   0.011   0.001   HIS B 266 
 PHE   0.020   0.001   PHE A 458 
 TYR   0.010   0.001   TYR B 479 
 ARG   0.004   0.000   ARG B 139 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8369 (pp20) cc_final: 0.7716 (pp20)
REVERT: A  399 TYR cc_start: 0.8506 (m-80) cc_final: 0.7857 (m-10)
REVERT: A  423 ASP cc_start: 0.8938 (t70) cc_final: 0.8483 (t0)
REVERT: A  444 GLU cc_start: 0.8514 (tp30) cc_final: 0.8207 (tm-30)
REVERT: A  591 MET cc_start: 0.8739 (tpp) cc_final: 0.8260 (tpt)
REVERT: B  284 LEU cc_start: 0.8997 (mt) cc_final: 0.8696 (mp)
REVERT: B  569 TYR cc_start: 0.8640 (t80) cc_final: 0.8220 (t80)
  outliers start: 8
  outliers final: 6
  residues processed: 109
  average time/residue: 0.1410
  time to fit residues: 24.4706
Evaluate side-chains
  109 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  422 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 98 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 94 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 101 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0570
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.084086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.069438 restraints weight = 23600.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.071679 restraints weight = 12658.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.073180 restraints weight = 8210.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8350  Z= 0.179
  Angle     :  0.546   8.821  11343  Z= 0.278
  Chirality :  0.042   0.187   1342
  Planarity :  0.004   0.041   1431
  Dihedral  :  8.851 141.514   1189
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.58 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.69 (0.26), residues: 1049
  helix:  1.04 (0.23), residues: 487
  sheet: -1.40 (0.37), residues: 185
  loop : -1.94 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B 602 
 HIS   0.003   0.001   HIS B 524 
 PHE   0.019   0.001   PHE B 433 
 TYR   0.009   0.001   TYR B 136 
 ARG   0.002   0.000   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8383 (pp20) cc_final: 0.7726 (pp20)
REVERT: A  151 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8694 (mp)
REVERT: A  399 TYR cc_start: 0.8481 (m-80) cc_final: 0.7829 (m-10)
REVERT: A  423 ASP cc_start: 0.8946 (t70) cc_final: 0.8680 (t0)
REVERT: A  444 GLU cc_start: 0.8488 (tp30) cc_final: 0.8201 (tm-30)
REVERT: A  591 MET cc_start: 0.8679 (tpp) cc_final: 0.8237 (tpt)
REVERT: B   73 MET cc_start: 0.8166 (tpt) cc_final: 0.7954 (tpt)
REVERT: B  164 MET cc_start: 0.8532 (mtp) cc_final: 0.8253 (mtm)
REVERT: B  284 LEU cc_start: 0.8980 (mt) cc_final: 0.8698 (mp)
  outliers start: 20
  outliers final: 11
  residues processed: 116
  average time/residue: 0.1410
  time to fit residues: 25.8378
Evaluate side-chains
  107 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  505 MET
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 289 HIS
B 419 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.081661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.065417 restraints weight = 33181.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.068002 restraints weight = 15637.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.069731 restraints weight = 9478.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8350  Z= 0.270
  Angle     :  0.575   7.810  11343  Z= 0.292
  Chirality :  0.043   0.137   1342
  Planarity :  0.004   0.041   1431
  Dihedral  :  9.054 142.252   1189
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.99 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.49 (0.26), residues: 1049
  helix:  1.18 (0.23), residues: 487
  sheet: -1.33 (0.37), residues: 186
  loop : -1.77 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.006   TRP B 602 
 HIS   0.004   0.001   HIS B 105 
 PHE   0.035   0.002   PHE A 458 
 TYR   0.036   0.001   TYR B 569 
 ARG   0.002   0.000   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8397 (pp20) cc_final: 0.7717 (pp20)
REVERT: A  151 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8714 (mp)
REVERT: A  296 MET cc_start: 0.8423 (mmt) cc_final: 0.8037 (mmp)
REVERT: A  399 TYR cc_start: 0.8531 (m-80) cc_final: 0.8316 (m-10)
REVERT: A  423 ASP cc_start: 0.9002 (t70) cc_final: 0.8756 (t0)
REVERT: A  444 GLU cc_start: 0.8595 (tp30) cc_final: 0.8262 (tm-30)
REVERT: A  591 MET cc_start: 0.8722 (tpp) cc_final: 0.8275 (tpt)
REVERT: B   73 MET cc_start: 0.8296 (tpt) cc_final: 0.8039 (tpt)
REVERT: B  284 LEU cc_start: 0.9099 (mt) cc_final: 0.8868 (mp)
REVERT: B  569 TYR cc_start: 0.8685 (t80) cc_final: 0.7972 (t80)
REVERT: B  573 MET cc_start: 0.8649 (mmm) cc_final: 0.8438 (mmm)
  outliers start: 18
  outliers final: 12
  residues processed: 105
  average time/residue: 0.1365
  time to fit residues: 22.6765
Evaluate side-chains
  105 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  505 MET
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0270
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.5838

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.083288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.067483 restraints weight = 28941.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.069950 restraints weight = 14170.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.071659 restraints weight = 8799.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3063
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3063 r_free = 0.3063    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3063 r_free = 0.3063    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3063
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8350  Z= 0.162
  Angle     :  0.553   9.932  11343  Z= 0.277
  Chirality :  0.041   0.142   1342
  Planarity :  0.004   0.041   1431
  Dihedral  :  9.078 143.081   1189
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.58 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.29 (0.26), residues: 1049
  helix:  1.28 (0.23), residues: 487
  sheet: -1.08 (0.38), residues: 186
  loop : -1.65 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP B 602 
 HIS   0.002   0.001   HIS A 539 
 PHE   0.029   0.001   PHE A 458 
 TYR   0.028   0.001   TYR B 569 
 ARG   0.001   0.000   ARG B 552 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8399 (pp20) cc_final: 0.7758 (pp20)
REVERT: A  148 ASP cc_start: 0.7741 (p0) cc_final: 0.7496 (p0)
REVERT: A  296 MET cc_start: 0.8478 (mmt) cc_final: 0.8121 (mmp)
REVERT: A  339 MET cc_start: 0.8657 (mmp) cc_final: 0.8408 (mmm)
REVERT: A  399 TYR cc_start: 0.8498 (m-80) cc_final: 0.8287 (m-10)
REVERT: A  423 ASP cc_start: 0.8973 (t70) cc_final: 0.8729 (t0)
REVERT: A  444 GLU cc_start: 0.8559 (tp30) cc_final: 0.8238 (tm-30)
REVERT: A  591 MET cc_start: 0.8687 (tpp) cc_final: 0.8247 (tpt)
REVERT: B  164 MET cc_start: 0.8488 (mtp) cc_final: 0.8156 (mtm)
REVERT: B  284 LEU cc_start: 0.9052 (mt) cc_final: 0.8791 (mp)
REVERT: B  569 TYR cc_start: 0.8702 (t80) cc_final: 0.7975 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 108
  average time/residue: 0.1434
  time to fit residues: 24.2242
Evaluate side-chains
  99 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0980
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.0186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.082525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.065468 restraints weight = 43006.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.068348 restraints weight = 18261.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.070281 restraints weight = 10488.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8350  Z= 0.208
  Angle     :  0.561   9.084  11343  Z= 0.280
  Chirality :  0.042   0.153   1342
  Planarity :  0.004   0.041   1431
  Dihedral  :  9.089 143.378   1189
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.65 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.26), residues: 1049
  helix:  1.29 (0.23), residues: 488
  sheet: -0.95 (0.38), residues: 184
  loop : -1.59 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B 602 
 HIS   0.003   0.001   HIS A 289 
 PHE   0.032   0.001   PHE A 458 
 TYR   0.029   0.001   TYR B 569 
 ARG   0.002   0.000   ARG B 570 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8458 (pp20) cc_final: 0.7815 (pp20)
REVERT: A  296 MET cc_start: 0.8480 (mmt) cc_final: 0.8088 (mmp)
REVERT: A  339 MET cc_start: 0.8704 (mmp) cc_final: 0.8418 (mmm)
REVERT: A  399 TYR cc_start: 0.8530 (m-80) cc_final: 0.8303 (m-10)
REVERT: A  423 ASP cc_start: 0.8993 (t70) cc_final: 0.8548 (t0)
REVERT: A  444 GLU cc_start: 0.8588 (tp30) cc_final: 0.8226 (tm-30)
REVERT: A  591 MET cc_start: 0.8700 (tpp) cc_final: 0.8256 (tpt)
REVERT: B  164 MET cc_start: 0.8550 (mtp) cc_final: 0.8241 (mtm)
REVERT: B  284 LEU cc_start: 0.9096 (mt) cc_final: 0.8843 (mp)
REVERT: B  569 TYR cc_start: 0.8668 (t80) cc_final: 0.8450 (t80)
  outliers start: 19
  outliers final: 14
  residues processed: 100
  average time/residue: 0.1318
  time to fit residues: 21.1486
Evaluate side-chains
  99 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 95 optimal weight:    0.4980
   chunk 93 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 37 optimal weight:    0.2980
   chunk 83 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.083522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.067379 restraints weight = 32985.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.070018 restraints weight = 15382.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.071801 restraints weight = 9248.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8350  Z= 0.167
  Angle     :  0.565  11.380  11343  Z= 0.279
  Chirality :  0.041   0.157   1342
  Planarity :  0.004   0.040   1431
  Dihedral  :  9.062 143.332   1189
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.36 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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 (0.26), residues: 1049
  helix:  1.34 (0.24), residues: 489
  sheet: -0.88 (0.38), residues: 184
  loop : -1.54 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B 602 
 HIS   0.002   0.001   HIS B 524 
 PHE   0.039   0.001   PHE B 433 
 TYR   0.027   0.001   TYR B 569 
 ARG   0.002   0.000   ARG B 381 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8469 (pp20) cc_final: 0.7841 (pp20)
REVERT: A  339 MET cc_start: 0.8740 (mmp) cc_final: 0.8482 (mmm)
REVERT: A  399 TYR cc_start: 0.8504 (m-80) cc_final: 0.8282 (m-10)
REVERT: A  423 ASP cc_start: 0.8968 (t70) cc_final: 0.8720 (t0)
REVERT: A  444 GLU cc_start: 0.8549 (tp30) cc_final: 0.8197 (tm-30)
REVERT: A  591 MET cc_start: 0.8673 (tpp) cc_final: 0.8253 (tpt)
REVERT: B  164 MET cc_start: 0.8555 (mtp) cc_final: 0.8259 (mtm)
REVERT: B  284 LEU cc_start: 0.9062 (mt) cc_final: 0.8809 (mp)
REVERT: B  569 TYR cc_start: 0.8603 (t80) cc_final: 0.8338 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 108
  average time/residue: 0.1399
  time to fit residues: 23.9968
Evaluate side-chains
  100 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 49 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0980
   chunk 105 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0040
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
A 600 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.084334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.067678 restraints weight = 40145.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.070506 restraints weight = 17523.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.072419 restraints weight = 10160.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8350  Z= 0.151
  Angle     :  0.568  14.656  11343  Z= 0.277
  Chirality :  0.041   0.159   1342
  Planarity :  0.003   0.040   1431
  Dihedral  :  8.996 144.011   1189
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.54 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.26), residues: 1049
  helix:  1.37 (0.24), residues: 489
  sheet: -0.68 (0.39), residues: 184
  loop : -1.44 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B 602 
 HIS   0.003   0.000   HIS B 524 
 PHE   0.031   0.001   PHE A 458 
 TYR   0.024   0.001   TYR B 569 
 ARG   0.001   0.000   ARG B 552 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8458 (pp20) cc_final: 0.7831 (pp20)
REVERT: A  339 MET cc_start: 0.8756 (mmp) cc_final: 0.8522 (mmm)
REVERT: A  399 TYR cc_start: 0.8501 (m-80) cc_final: 0.7833 (m-10)
REVERT: A  423 ASP cc_start: 0.8939 (t70) cc_final: 0.8696 (t0)
REVERT: A  444 GLU cc_start: 0.8542 (tp30) cc_final: 0.8200 (tm-30)
REVERT: A  591 MET cc_start: 0.8648 (tpp) cc_final: 0.8258 (tpt)
REVERT: B  106 ASP cc_start: 0.8787 (t0) cc_final: 0.8204 (t0)
REVERT: B  284 LEU cc_start: 0.9038 (mt) cc_final: 0.8750 (mp)
REVERT: B  569 TYR cc_start: 0.8565 (t80) cc_final: 0.8272 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1506
  time to fit residues: 25.0766
Evaluate side-chains
  106 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 97 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 92 optimal weight:    0.0040
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
B 105 HIS
B 271 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.084177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.068484 restraints weight = 28609.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.070961 restraints weight = 14061.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.072636 restraints weight = 8712.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3081
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8350  Z= 0.169
  Angle     :  0.566  15.469  11343  Z= 0.278
  Chirality :  0.041   0.166   1342
  Planarity :  0.003   0.040   1431
  Dihedral  :  9.167 148.381   1189
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.42 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.07 (0.27), residues: 1049
  helix:  1.42 (0.24), residues: 489
  sheet: -0.68 (0.39), residues: 184
  loop : -1.40 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 602 
 HIS   0.002   0.001   HIS B 524 
 PHE   0.040   0.001   PHE A 458 
 TYR   0.022   0.001   TYR B 569 
 ARG   0.001   0.000   ARG B 552 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8445 (pp20) cc_final: 0.7814 (pp20)
REVERT: A  339 MET cc_start: 0.8760 (mmp) cc_final: 0.8502 (mmm)
REVERT: A  399 TYR cc_start: 0.8497 (m-80) cc_final: 0.8282 (m-10)
REVERT: A  423 ASP cc_start: 0.8951 (t70) cc_final: 0.8500 (t0)
REVERT: A  444 GLU cc_start: 0.8561 (tp30) cc_final: 0.8228 (tm-30)
REVERT: A  516 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8026 (mp10)
REVERT: A  556 MET cc_start: 0.9154 (tpp) cc_final: 0.8911 (tpp)
REVERT: A  591 MET cc_start: 0.8658 (tpp) cc_final: 0.8265 (tpt)
REVERT: B  106 ASP cc_start: 0.8755 (t0) cc_final: 0.8205 (t0)
REVERT: B  284 LEU cc_start: 0.9036 (mt) cc_final: 0.8742 (mp)
REVERT: B  569 TYR cc_start: 0.8559 (t80) cc_final: 0.8247 (t80)
  outliers start: 16
  outliers final: 13
  residues processed: 102
  average time/residue: 0.1366
  time to fit residues: 21.9179
Evaluate side-chains
  106 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  516 GLN
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0010
   chunk 43 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 47 optimal weight:    0.2980
   chunk 62 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 102 optimal weight:    8.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 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 = 0.3320 r_free = 0.3320 target = 0.084501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.069602 restraints weight = 23573.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.071869 restraints weight = 12519.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.073389 restraints weight = 8096.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8350  Z= 0.160
  Angle     :  0.569  14.672  11343  Z= 0.282
  Chirality :  0.041   0.159   1342
  Planarity :  0.003   0.040   1431
  Dihedral  :  9.057 143.954   1189
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.77 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.09 (0.27), residues: 1049
  helix:  1.42 (0.24), residues: 489
  sheet: -0.64 (0.39), residues: 184
  loop : -1.36 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 602 
 HIS   0.002   0.001   HIS B 524 
 PHE   0.041   0.002   PHE A 458 
 TYR   0.022   0.001   TYR B 569 
 ARG   0.001   0.000   ARG B 552 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8443 (pp20) cc_final: 0.7805 (pp20)
REVERT: A  296 MET cc_start: 0.8323 (mmt) cc_final: 0.7997 (mmp)
REVERT: A  339 MET cc_start: 0.8711 (mmp) cc_final: 0.8483 (mmm)
REVERT: A  399 TYR cc_start: 0.8487 (m-80) cc_final: 0.8273 (m-10)
REVERT: A  423 ASP cc_start: 0.8933 (t70) cc_final: 0.8487 (t0)
REVERT: A  444 GLU cc_start: 0.8554 (tp30) cc_final: 0.8228 (tm-30)
REVERT: A  516 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8033 (mp10)
REVERT: A  591 MET cc_start: 0.8638 (tpp) cc_final: 0.8266 (tpt)
REVERT: B  106 ASP cc_start: 0.8790 (t0) cc_final: 0.8205 (t0)
REVERT: B  284 LEU cc_start: 0.9009 (mt) cc_final: 0.8711 (mp)
REVERT: B  569 TYR cc_start: 0.8544 (t80) cc_final: 0.8237 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 103
  average time/residue: 0.1358
  time to fit residues: 22.2869
Evaluate side-chains
  109 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  516 GLN
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    0.1980
   chunk 63 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 406 HIS
** B 168 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 = 0.3316 r_free = 0.3316 target = 0.084236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.067950 restraints weight = 33941.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.070607 restraints weight = 15840.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.072417 restraints weight = 9526.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8350  Z= 0.173
  Angle     :  0.580  15.419  11343  Z= 0.288
  Chirality :  0.041   0.151   1342
  Planarity :  0.004   0.040   1431
  Dihedral  :  9.017 142.996   1189
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.65 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.13 (0.27), residues: 1049
  helix:  1.45 (0.24), residues: 488
  sheet: -0.65 (0.39), residues: 184
  loop : -1.32 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 602 
 HIS   0.002   0.001   HIS B 524 
 PHE   0.040   0.001   PHE A 458 
 TYR   0.021   0.001   TYR B 569 
 ARG   0.002   0.000   ARG B 552 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2654.17 seconds
wall clock time: 48 minutes 37.08 seconds (2917.08 seconds total)