Starting phenix.real_space_refine
on Sat Aug 23 02:43:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ips_35642/08_2025/8ips_35642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ips_35642/08_2025/8ips_35642.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ips_35642/08_2025/8ips_35642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ips_35642/08_2025/8ips_35642.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ips_35642/08_2025/8ips_35642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ips_35642/08_2025/8ips_35642.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      30      5.16       5
     C    5823      2.51       5
     N    1591      2.21       5
     O    1626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9071
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4433
          Classifications: {'peptide': 573}
          Link IDs: {'PTRANS': 18, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 4595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4595
          Classifications: {'peptide': 588}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 560}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.39, per 1000 atoms: 0.26
  Number of scatterers: 9071
  At special positions: 0
  Unit cell: (85.44, 92.16, 144.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      30     16.00
     O    1626      8.00
     N    1591      7.00
     C    5823      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 353.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 4 sheets defined
      62.3% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 9
    Processing helix  chain 'A' and resid 10 through 13
      removed outlier: 4.067A  pdb=" N   ARG A  13 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 10 through 13'
    Processing helix  chain 'A' and resid 15 through 50
      removed outlier: 3.532A  pdb=" N   GLY A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 54
      removed outlier: 3.597A  pdb=" N   LEU A  54 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 51 through 54'
    Processing helix  chain 'A' and resid 60 through 104
      removed outlier: 4.102A  pdb=" N   ALA A  64 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   GLY A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   VAL A  66 " --> pdb=" O   PRO A  62 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ALA A  70 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   PHE A  89 " --> pdb=" O   HIS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 157
      Proline residue:  A 140  - end of helix
    Processing helix  chain 'A' and resid 159 through 181
      removed outlier: 3.651A  pdb=" N   ALA A 163 " --> pdb=" O   ASP A 159 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   MET A 177 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 183 through 210
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 4.235A  pdb=" N   ILE A 215 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 266
      removed outlier: 3.587A  pdb=" N   LEU A 243 " --> pdb=" O   ARG A 239 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   LEU A 246 " --> pdb=" O   GLU A 242 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER A 247 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLN A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 292
      removed outlier: 3.741A  pdb=" N   PHE A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 299
      removed outlier: 3.702A  pdb=" N   THR A 298 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLY A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 294 through 299'
    Processing helix  chain 'A' and resid 300 through 302
      No H-bonds generated for 'chain 'A' and resid 300 through 302'
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 378 through 387
      removed outlier: 3.510A  pdb=" N   THR A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 415
    Processing helix  chain 'A' and resid 429 through 435
    Processing helix  chain 'A' and resid 442 through 452
    Processing helix  chain 'A' and resid 476 through 491
      removed outlier: 4.126A  pdb=" N   ARG A 482 " --> pdb=" O   GLY A 478 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LEU A 483 " --> pdb=" O   GLU A 479 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA A 486 " --> pdb=" O   ARG A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 520
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'B' and resid 2 through 16
      removed outlier: 3.689A  pdb=" N   GLN B   6 " --> pdb=" O   ASN B   2 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU B   8 " --> pdb=" O   SER B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 54
    Processing helix  chain 'B' and resid 58 through 62
      removed outlier: 3.543A  pdb=" N   LEU B  62 " --> pdb=" O   ARG B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 110
      removed outlier: 4.329A  pdb=" N   LEU B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   LEU B  69 " --> pdb=" O   PRO B  65 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL B  70 " --> pdb=" O   PHE B  66 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ILE B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLY B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 115
    Processing helix  chain 'B' and resid 120 through 159
      removed outlier: 3.942A  pdb=" N   ASP B 132 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   MET B 133 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   HIS B 134 " --> pdb=" O   ILE B 130 " (cutoff:3.500A)
      Proline residue:  B 142  - end of helix
      removed outlier: 3.940A  pdb=" N   VAL B 148 " --> pdb=" O   MET B 144 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER B 149 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      Proline residue:  B 151  - end of helix
    Processing helix  chain 'B' and resid 164 through 183
      removed outlier: 3.841A  pdb=" N   THR B 172 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ALA B 173 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
      Proline residue:  B 177  - end of helix
    Processing helix  chain 'B' and resid 189 through 211
      removed outlier: 3.674A  pdb=" N   ARG B 193 " --> pdb=" O   ASP B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 218
      removed outlier: 3.745A  pdb=" N   ILE B 217 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   PHE B 218 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 240
      removed outlier: 4.039A  pdb=" N   ILE B 228 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG B 229 " --> pdb=" O   ILE B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 247
      removed outlier: 3.584A  pdb=" N   PHE B 247 " --> pdb=" O   LEU B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 272
      removed outlier: 3.774A  pdb=" N   GLY B 251 " --> pdb=" O   PHE B 247 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   TYR B 272 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 310
      Proline residue:  B 298  - end of helix
      removed outlier: 4.105A  pdb=" N   PHE B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
      Proline residue:  B 303  - end of helix
      removed outlier: 3.556A  pdb=" N   LEU B 307 " --> pdb=" O   PRO B 303 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   THR B 309 " --> pdb=" O   ARG B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 329
      removed outlier: 3.908A  pdb=" N   GLY B 319 " --> pdb=" O   ALA B 315 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA B 320 " --> pdb=" O   GLN B 316 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER B 323 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 390
      No H-bonds generated for 'chain 'B' and resid 388 through 390'
    Processing helix  chain 'B' and resid 391 through 397
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 438 through 444
    Processing helix  chain 'B' and resid 480 through 484
      removed outlier: 4.011A  pdb=" N   ALA B 483 " --> pdb=" O   GLY B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 491
      removed outlier: 3.519A  pdb=" N   ALA B 491 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 502
      removed outlier: 3.537A  pdb=" N   ALA B 497 " --> pdb=" O   ARG B 493 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ASN B 502 " --> pdb=" O   ARG B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 533
    Processing helix  chain 'B' and resid 566 through 571
    Processing helix  chain 'B' and resid 575 through 588
      removed outlier: 3.940A  pdb=" N   ILE B 588 " --> pdb=" O   ARG B 584 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 362
      removed outlier: 3.952A  pdb=" N   ARG A 342 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   GLU A 396 " --> pdb=" O   ARG A 342 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 416 through 419
      removed outlier: 6.352A  pdb=" N   SER A 417 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLN A 541 " --> pdb=" O   HIS A 368 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA A 370 " --> pdb=" O   GLN A 541 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   ILE A 542 " --> pdb=" O   GLN A 553 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   GLN A 553 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   VAL A 544 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 551 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 370 through 373
      removed outlier: 3.912A  pdb=" N   PHE B 371 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE B 350 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   ALA B 352 " --> pdb=" O   ARG B 407 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   ARG B 407 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   ASP B 354 " --> pdb=" O   SER B 405 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   SER B 405 " --> pdb=" O   ASP B 354 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   SER B 401 " --> pdb=" O   THR B 358 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE B 411 " --> pdb=" O   ILE B 408 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 425 through 428
      removed outlier: 6.226A  pdb=" N   SER B 426 " --> pdb=" O   LEU B 508 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ASP B 510 " --> pdb=" O   SER B 426 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   VAL B 428 " --> pdb=" O   ASP B 510 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LEU B 507 " --> pdb=" O   LEU B 538 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   VAL B 540 " --> pdb=" O   LEU B 507 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU B 509 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   ARG B 378 " --> pdb=" O   VAL B 552 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   TRP B 554 " --> pdb=" O   ARG B 378 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   VAL B 380 " --> pdb=" O   TRP B 554 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   MET B 556 " --> pdb=" O   VAL B 380 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   VAL B 382 " --> pdb=" O   MET B 556 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ILE B 553 " --> pdb=" O   GLN B 564 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLN B 564 " --> pdb=" O   ILE B 553 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   VAL B 555 " --> pdb=" O   ILE B 562 " (cutoff:3.500A)

    497 hydrogen bonds defined for protein.
    1470 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.20 -     1.37: 3157
        1.37 -     1.55: 6038
        1.55 -     1.73: 0
        1.73 -     1.91: 58
        1.91 -     2.09: 3
  Bond restraints: 9256
  Sorted by residual:
  bond pdb=" C3C HEM A 601 "
       pdb=" CAC HEM A 601 "
    ideal  model  delta    sigma   weight residual
    1.544  1.450  0.094 2.00e-02 2.50e+03 2.20e+01
  bond pdb=" C3B HEM A 601 "
       pdb=" CAB HEM A 601 "
    ideal  model  delta    sigma   weight residual
    1.544  1.454  0.090 2.00e-02 2.50e+03 2.01e+01
  bond pdb=" C   ILE B  48 "
       pdb=" O   ILE B  48 "
    ideal  model  delta    sigma   weight residual
    1.237  1.196  0.041 1.12e-02 7.97e+03 1.34e+01
  bond pdb=" N   ILE B  38 "
       pdb=" CA  ILE B  38 "
    ideal  model  delta    sigma   weight residual
    1.461  1.502 -0.041 1.17e-02 7.31e+03 1.24e+01
  bond pdb=" CA  ALA B  42 "
       pdb=" CB  ALA B  42 "
    ideal  model  delta    sigma   weight residual
    1.529  1.475  0.054 1.55e-02 4.16e+03 1.21e+01
  ... (remaining 9251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 12194
        1.75 -     3.50: 300
        3.50 -     5.25: 70
        5.25 -     7.00: 15
        7.00 -     8.75: 9
  Bond angle restraints: 12588
  Sorted by residual:
  angle pdb=" CA  PHE B 467 "
        pdb=" CB  PHE B 467 "
        pdb=" CG  PHE B 467 "
      ideal   model   delta    sigma   weight residual
     113.80  118.89   -5.09 1.00e+00 1.00e+00 2.59e+01
  angle pdb=" C   GLN B  50 "
        pdb=" CA  GLN B  50 "
        pdb=" CB  GLN B  50 "
      ideal   model   delta    sigma   weight residual
     110.67  102.36    8.31 1.92e+00 2.71e-01 1.87e+01
  angle pdb=" C   ILE B  36 "
        pdb=" N   LEU B  37 "
        pdb=" CA  LEU B  37 "
      ideal   model   delta    sigma   weight residual
     120.29  114.24    6.05 1.42e+00 4.96e-01 1.81e+01
  angle pdb=" CA  ILE B  48 "
        pdb=" C   ILE B  48 "
        pdb=" O   ILE B  48 "
      ideal   model   delta    sigma   weight residual
     121.05  116.37    4.68 1.11e+00 8.12e-01 1.78e+01
  angle pdb=" CA  LEU B  37 "
        pdb=" C   LEU B  37 "
        pdb=" O   LEU B  37 "
      ideal   model   delta    sigma   weight residual
     120.42  116.42    4.00 1.06e+00 8.90e-01 1.42e+01
  ... (remaining 12583 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4637
       17.97 -    35.94: 645
       35.94 -    53.90: 177
       53.90 -    71.87: 34
       71.87 -    89.84: 16
  Dihedral angle restraints: 5509
    sinusoidal: 2178
      harmonic: 3331
  Sorted by residual:
  dihedral pdb=" C2C HEM A 601 "
           pdb=" C3C HEM A 601 "
           pdb=" CAC HEM A 601 "
           pdb=" CBC HEM A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -100.00  -80.00     2      1.00e+01 1.00e-02 4.66e+01
  dihedral pdb=" C2B HEM A 601 "
           pdb=" C3B HEM A 601 "
           pdb=" CAB HEM A 601 "
           pdb=" CBB HEM A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  114.26   65.74     2      1.00e+01 1.00e-02 3.99e+01
  dihedral pdb=" CA  ASP A 461 "
           pdb=" C   ASP A 461 "
           pdb=" N   ALA A 462 "
           pdb=" CA  ALA A 462 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.28   17.72     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 5506 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 908
       0.029 -    0.059: 346
       0.059 -    0.088: 121
       0.088 -    0.117: 68
       0.117 -    0.146: 13
  Chirality restraints: 1456
  Sorted by residual:
  chirality pdb=" CA  GLN B  50 "
            pdb=" N   GLN B  50 "
            pdb=" C   GLN B  50 "
            pdb=" CB  GLN B  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.35e-01
  chirality pdb=" CA  LEU B  37 "
            pdb=" N   LEU B  37 "
            pdb=" C   LEU B  37 "
            pdb=" CB  LEU B  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.07e-01
  chirality pdb=" CG  LEU A 120 "
            pdb=" CB  LEU A 120 "
            pdb=" CD1 LEU A 120 "
            pdb=" CD2 LEU A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.87e-01
  ... (remaining 1453 not shown)

  Planarity restraints: 1608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 173 "    0.048 5.00e-02 4.00e+02   7.34e-02 8.63e+00
        pdb=" N   PRO B 174 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 174 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 174 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 176 "   -0.042 5.00e-02 4.00e+02   6.35e-02 6.46e+00
        pdb=" N   PRO B 177 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 177 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 177 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  36 "    0.012 2.00e-02 2.50e+03   2.38e-02 5.68e+00
        pdb=" C   ILE B  36 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ILE B  36 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU B  37 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1605 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1327
        2.76 -     3.29: 8561
        3.29 -     3.83: 14359
        3.83 -     4.36: 14981
        4.36 -     4.90: 27360
  Nonbonded interactions: 66588
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 129 "
            pdb=" OG  SER B 323 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" NE2 GLN A  93 "
            pdb=" OG  SER B 232 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OG  SER A 427 "
            pdb=" OD2 ASP B 207 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" NE2 GLN A 563 "
            pdb=" O   GLY A 564 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OD1 ASP B 460 "
            pdb=" N   ASN B 461 "
     model   vdw
     2.271 3.120
  ... (remaining 66583 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.880
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
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      :  0.005   0.229   9257  Z= 0.256
  Angle     :  0.703   8.754  12588  Z= 0.382
  Chirality :  0.040   0.146   1456
  Planarity :  0.005   0.073   1608
  Dihedral  : 18.308  89.837   3361
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 30.01 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.26), residues: 1157
  helix:  1.79 (0.22), residues: 636
  sheet:  0.04 (0.65), residues: 73
  loop : -2.28 (0.25), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 485 
 TYR   0.016   0.001   TYR A 134 
 PHE   0.022   0.001   PHE B 467 
 TRP   0.014   0.001   TRP A  41 
 HIS   0.003   0.001   HIS A  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 9256)
  covalent geometry    : angle       0.70291 (12588)
  hydrogen bonds       : bond        0.15228 (  497)
  hydrogen bonds       : angle       5.29585 ( 1470)
  Misc. bond           : bond        0.03554 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  149 MET cc_start: 0.7147 (mmm) cc_final: 0.6905 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 79
  average time/residue: 0.1104
  time to fit residues: 12.0093
Evaluate side-chains
  63 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue  488 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 547 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.106074 restraints weight = 14905.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.106666 restraints weight = 13189.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.107437 restraints weight = 11544.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.107870 restraints weight = 9698.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.108106 restraints weight = 8715.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.0947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.141   9257  Z= 0.178
  Angle     :  0.643  13.766  12588  Z= 0.317
  Chirality :  0.040   0.155   1456
  Planarity :  0.005   0.059   1608
  Dihedral  :  5.948  78.763   1277
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 29.37 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.25), residues: 1157
  helix:  2.01 (0.21), residues: 636
  sheet: -0.58 (0.69), residues: 58
  loop : -2.15 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 493 
 TYR   0.017   0.002   TYR A 134 
 PHE   0.019   0.001   PHE A 164 
 TRP   0.010   0.001   TRP A  41 
 HIS   0.008   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9256)
  covalent geometry    : angle       0.64282 (12588)
  hydrogen bonds       : bond        0.08046 (  497)
  hydrogen bonds       : angle       4.46152 ( 1470)
  Misc. bond           : bond        0.14110 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 67
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  528 MET cc_start: 0.8589 (ptt) cc_final: 0.8340 (ptt)
REVERT: B    1 MET cc_start: 0.6706 (tmm) cc_final: 0.6004 (pmm)
REVERT: B  129 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8050 (mt0)
REVERT: B  225 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7964 (tt)
  outliers start: 39
  outliers final: 24
  residues processed: 101
  average time/residue: 0.0975
  time to fit residues: 13.5251
Evaluate side-chains
  87 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  164 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  545 MET
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  129 GLN
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 MET
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  363 LYS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  555 VAL
Chi-restraints excluded: chain B residue  572 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 85 optimal weight:    0.0010
   chunk 26 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0770
   chunk 2 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.4344

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.137518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.110840 restraints weight = 14721.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.111108 restraints weight = 12611.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.111623 restraints weight = 10736.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.111945 restraints weight = 9555.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.112052 restraints weight = 8846.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9257  Z= 0.138
  Angle     :  0.571  12.025  12588  Z= 0.283
  Chirality :  0.038   0.147   1456
  Planarity :  0.005   0.050   1608
  Dihedral  :  5.939  80.250   1277
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.66 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 29.80 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.26), residues: 1157
  helix:  2.14 (0.21), residues: 649
  sheet: -0.17 (0.70), residues: 56
  loop : -2.13 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 115 
 TYR   0.016   0.001   TYR A 134 
 PHE   0.014   0.001   PHE A 164 
 TRP   0.012   0.001   TRP A  41 
 HIS   0.005   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9256)
  covalent geometry    : angle       0.57112 (12588)
  hydrogen bonds       : bond        0.06924 (  497)
  hydrogen bonds       : angle       4.19761 ( 1470)
  Misc. bond           : bond        0.04151 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 66
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  527 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8109 (tt)
REVERT: B    1 MET cc_start: 0.6576 (tmm) cc_final: 0.5914 (pmm)
REVERT: B   19 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7787 (mt)
  outliers start: 40
  outliers final: 22
  residues processed: 101
  average time/residue: 0.0788
  time to fit residues: 11.9121
Evaluate side-chains
  88 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 64
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  164 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  363 LYS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  572 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 93 optimal weight:    0.4980
   chunk 77 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0010
   chunk 7 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.6588

-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.136784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.109488 restraints weight = 15047.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109420 restraints weight = 14560.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.110543 restraints weight = 11830.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.110894 restraints weight = 9576.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.111157 restraints weight = 8928.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9257  Z= 0.139
  Angle     :  0.568  10.587  12588  Z= 0.278
  Chirality :  0.038   0.145   1456
  Planarity :  0.004   0.045   1608
  Dihedral  :  5.840  78.147   1277
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.26 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 30.22 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.26), residues: 1157
  helix:  2.19 (0.21), residues: 649
  sheet: -0.48 (0.68), residues: 58
  loop : -2.11 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 115 
 TYR   0.017   0.001   TYR A 134 
 PHE   0.015   0.001   PHE A 164 
 TRP   0.011   0.001   TRP A  41 
 HIS   0.004   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9256)
  covalent geometry    : angle       0.56814 (12588)
  hydrogen bonds       : bond        0.06915 (  497)
  hydrogen bonds       : angle       4.10951 ( 1470)
  Misc. bond           : bond        0.03457 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 67
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  569 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7215 (m-80)
REVERT: B    1 MET cc_start: 0.6645 (tmm) cc_final: 0.5955 (pmm)
REVERT: B   19 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7839 (mt)
  outliers start: 45
  outliers final: 28
  residues processed: 104
  average time/residue: 0.0897
  time to fit residues: 13.5570
Evaluate side-chains
  93 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 63
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  164 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  569 PHE
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 MET
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  441 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  511 GLU
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  555 VAL
Chi-restraints excluded: chain B residue  572 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0270
   chunk 97 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 104 optimal weight:    4.9990
   overall best weight:    1.3244

-------------------------------------------------------------------------------
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 = 0.3702 r_free = 0.3702 target = 0.132154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.104463 restraints weight = 14984.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.105061 restraints weight = 13168.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.106081 restraints weight = 10887.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106238 restraints weight = 9021.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.106577 restraints weight = 8727.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   9257  Z= 0.184
  Angle     :  0.632  14.470  12588  Z= 0.307
  Chirality :  0.040   0.159   1456
  Planarity :  0.005   0.049   1608
  Dihedral  :  5.921  76.397   1277
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.52 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 30.65 %
    Favored  : 64.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.26), residues: 1157
  helix:  2.08 (0.21), residues: 650
  sheet: -0.73 (0.67), residues: 58
  loop : -2.15 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 115 
 TYR   0.018   0.002   TYR A 134 
 PHE   0.019   0.001   PHE A 164 
 TRP   0.013   0.001   TRP B 427 
 HIS   0.005   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 9256)
  covalent geometry    : angle       0.63165 (12588)
  hydrogen bonds       : bond        0.08130 (  497)
  hydrogen bonds       : angle       4.27421 ( 1470)
  Misc. bond           : bond        0.07901 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 65
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8395 (t)
REVERT: B    1 MET cc_start: 0.6539 (tmm) cc_final: 0.5972 (pmm)
  outliers start: 49
  outliers final: 34
  residues processed: 108
  average time/residue: 0.0826
  time to fit residues: 12.9940
Evaluate side-chains
  97 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 62
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  164 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  451 ARG
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 MET
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  441 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  511 GLU
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  555 VAL
Chi-restraints excluded: chain B residue  572 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.131801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.103396 restraints weight = 14947.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.104171 restraints weight = 12145.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104938 restraints weight = 10458.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.106180 restraints weight = 8664.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.106293 restraints weight = 8004.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   9257  Z= 0.182
  Angle     :  0.630  14.015  12588  Z= 0.308
  Chirality :  0.040   0.143   1456
  Planarity :  0.004   0.046   1608
  Dihedral  :  5.946  76.693   1277
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.09 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 31.28 %
    Favored  : 63.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1157
  helix:  1.99 (0.21), residues: 656
  sheet: -0.79 (0.66), residues: 58
  loop : -2.16 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 115 
 TYR   0.017   0.001   TYR A 134 
 PHE   0.019   0.001   PHE A 164 
 TRP   0.012   0.001   TRP B 427 
 HIS   0.004   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 9256)
  covalent geometry    : angle       0.63038 (12588)
  hydrogen bonds       : bond        0.08161 (  497)
  hydrogen bonds       : angle       4.28137 ( 1470)
  Misc. bond           : bond        0.07177 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 62
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8391 (t)
REVERT: B    1 MET cc_start: 0.6560 (tmm) cc_final: 0.6026 (pmm)
REVERT: B  185 MET cc_start: 0.7676 (ttp) cc_final: 0.7434 (ttm)
REVERT: B  225 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8021 (tt)
REVERT: B  263 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8940 (mm)
  outliers start: 48
  outliers final: 40
  residues processed: 105
  average time/residue: 0.0891
  time to fit residues: 13.6033
Evaluate side-chains
  103 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 60
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  164 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  451 ARG
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  179 PHE
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  441 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  500 LEU
Chi-restraints excluded: chain B residue  511 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  555 VAL
Chi-restraints excluded: chain B residue  572 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   chunk 103 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   chunk 88 optimal weight:   10.0000
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.135165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.107994 restraints weight = 14898.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.108470 restraints weight = 13072.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.109107 restraints weight = 11928.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.109366 restraints weight = 10002.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.110875 restraints weight = 8988.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9257  Z= 0.141
  Angle     :  0.579  11.452  12588  Z= 0.282
  Chirality :  0.038   0.142   1456
  Planarity :  0.004   0.044   1608
  Dihedral  :  5.899  79.275   1277
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.74 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 30.97 %
    Favored  : 63.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.26), residues: 1157
  helix:  2.16 (0.21), residues: 659
  sheet: -0.70 (0.67), residues: 58
  loop : -2.09 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 115 
 TYR   0.016   0.001   TYR A 134 
 PHE   0.015   0.001   PHE A 164 
 TRP   0.013   0.001   TRP A  41 
 HIS   0.004   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9256)
  covalent geometry    : angle       0.57852 (12588)
  hydrogen bonds       : bond        0.07107 (  497)
  hydrogen bonds       : angle       4.08625 ( 1470)
  Misc. bond           : bond        0.03407 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 69
  time to evaluate  : 0.281 
Fit side-chains
REVERT: B    1 MET cc_start: 0.6670 (tmm) cc_final: 0.6103 (pmm)
REVERT: B   19 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7911 (mt)
REVERT: B  129 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8097 (mt0)
REVERT: B  185 MET cc_start: 0.7736 (ttp) cc_final: 0.7503 (ttm)
  outliers start: 48
  outliers final: 33
  residues processed: 114
  average time/residue: 0.0826
  time to fit residues: 13.6296
Evaluate side-chains
  100 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 65
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  164 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue  129 GLN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  179 PHE
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  316 GLN
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  511 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  555 VAL
Chi-restraints excluded: chain B residue  572 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.134995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.107756 restraints weight = 14933.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.108328 restraints weight = 13120.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.109118 restraints weight = 11579.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.109755 restraints weight = 9737.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109855 restraints weight = 8664.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9257  Z= 0.146
  Angle     :  0.596  11.307  12588  Z= 0.291
  Chirality :  0.038   0.142   1456
  Planarity :  0.004   0.043   1608
  Dihedral  :  5.870  78.861   1277
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.91 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 30.75 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.26), residues: 1157
  helix:  2.14 (0.21), residues: 660
  sheet: -0.73 (0.66), residues: 58
  loop : -2.07 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 493 
 TYR   0.016   0.001   TYR A 134 
 PHE   0.016   0.001   PHE A 164 
 TRP   0.011   0.001   TRP A  41 
 HIS   0.004   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9256)
  covalent geometry    : angle       0.59630 (12588)
  hydrogen bonds       : bond        0.07179 (  497)
  hydrogen bonds       : angle       4.05888 ( 1470)
  Misc. bond           : bond        0.04080 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 65
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.6651 (tmm) cc_final: 0.6097 (pmm)
REVERT: B   19 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7896 (mt)
REVERT: B  129 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8116 (mt0)
REVERT: B  185 MET cc_start: 0.7788 (ttp) cc_final: 0.7563 (ttm)
REVERT: B  263 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8879 (mm)
  outliers start: 47
  outliers final: 38
  residues processed: 108
  average time/residue: 0.0858
  time to fit residues: 13.5858
Evaluate side-chains
  104 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 63
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  164 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  451 ARG
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue  129 GLN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  179 PHE
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  500 LEU
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  511 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  555 VAL
Chi-restraints excluded: chain B residue  572 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    0.2980
   chunk 10 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   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 = 0.3748 r_free = 0.3748 target = 0.136162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.108981 restraints weight = 14854.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.109270 restraints weight = 13259.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109905 restraints weight = 12255.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.110171 restraints weight = 10175.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.111756 restraints weight = 9159.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9257  Z= 0.138
  Angle     :  0.584  11.050  12588  Z= 0.283
  Chirality :  0.038   0.142   1456
  Planarity :  0.004   0.046   1608
  Dihedral  :  5.828  79.155   1277
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.74 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 30.97 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.26), residues: 1157
  helix:  2.23 (0.21), residues: 659
  sheet: -0.73 (0.66), residues: 58
  loop : -2.01 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 493 
 TYR   0.016   0.001   TYR A 134 
 PHE   0.015   0.001   PHE A 164 
 TRP   0.012   0.001   TRP A  41 
 HIS   0.004   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9256)
  covalent geometry    : angle       0.58368 (12588)
  hydrogen bonds       : bond        0.06814 (  497)
  hydrogen bonds       : angle       3.99193 ( 1470)
  Misc. bond           : bond        0.03087 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 66
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.6639 (tmm) cc_final: 0.6096 (pmm)
REVERT: B   19 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7892 (mt)
REVERT: B  185 MET cc_start: 0.7754 (ttp) cc_final: 0.7533 (ttm)
  outliers start: 44
  outliers final: 36
  residues processed: 107
  average time/residue: 0.0774
  time to fit residues: 12.0944
Evaluate side-chains
  102 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 65
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  164 PHE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  451 ARG
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  179 PHE
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  441 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  500 LEU
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  511 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  555 VAL
Chi-restraints excluded: chain B residue  572 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 94 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.132119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.104586 restraints weight = 14919.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.105841 restraints weight = 13035.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.106966 restraints weight = 10965.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.107208 restraints weight = 9107.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.107365 restraints weight = 8366.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   9257  Z= 0.184
  Angle     :  0.643  13.854  12588  Z= 0.312
  Chirality :  0.040   0.142   1456
  Planarity :  0.004   0.044   1608
  Dihedral  :  5.900  77.081   1277
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.83 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 31.07 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.26), residues: 1157
  helix:  2.12 (0.21), residues: 652
  sheet: -0.88 (0.65), residues: 58
  loop : -2.12 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 493 
 TYR   0.017   0.001   TYR A 134 
 PHE   0.019   0.001   PHE A 164 
 TRP   0.012   0.001   TRP B 427 
 HIS   0.004   0.001   HIS A  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9256)
  covalent geometry    : angle       0.64332 (12588)
  hydrogen bonds       : bond        0.08044 (  497)
  hydrogen bonds       : angle       4.20037 ( 1470)
  Misc. bond           : bond        0.06984 (    1)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 64
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.6720 (tmm) cc_final: 0.6084 (pmm)
REVERT: B  185 MET cc_start: 0.7756 (ttp) cc_final: 0.7550 (ttm)
REVERT: B  263 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8926 (mm)
REVERT: B  510 ASP cc_start: 0.7751 (t0) cc_final: 0.7535 (t0)
  outliers start: 43
  outliers final: 38
  residues processed: 103
  average time/residue: 0.0983
  time to fit residues: 14.2300
Evaluate side-chains
  101 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 62
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  164 PHE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  451 ARG
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  545 MET
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   66 PHE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  134 HIS
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  179 PHE
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  500 LEU
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  511 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  555 VAL
Chi-restraints excluded: chain B residue  572 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 94 optimal weight:    0.4980
   chunk 72 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   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 = 0.3742 r_free = 0.3742 target = 0.135491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108604 restraints weight = 14542.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.110044 restraints weight = 12282.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.111216 restraints weight = 10232.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.111361 restraints weight = 8471.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.111469 restraints weight = 7976.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9257  Z= 0.141
  Angle     :  0.603  11.782  12588  Z= 0.292
  Chirality :  0.038   0.176   1456
  Planarity :  0.004   0.043   1608
  Dihedral  :  5.836  77.197   1277
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.40 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 31.50 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.26), residues: 1157
  helix:  2.28 (0.21), residues: 654
  sheet: -0.34 (0.64), residues: 68
  loop : -2.11 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 115 
 TYR   0.016   0.001   TYR A 134 
 PHE   0.014   0.001   PHE A 164 
 TRP   0.014   0.001   TRP A  41 
 HIS   0.003   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9256)
  covalent geometry    : angle       0.60293 (12588)
  hydrogen bonds       : bond        0.07054 (  497)
  hydrogen bonds       : angle       4.03408 ( 1470)
  Misc. bond           : bond        0.02852 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1329.31 seconds
wall clock time: 23 minutes 38.12 seconds (1418.12 seconds total)