Starting phenix.real_space_refine
on Wed Sep 17 14:36:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iqf_60790/09_2025/9iqf_60790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iqf_60790/09_2025/9iqf_60790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iqf_60790/09_2025/9iqf_60790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iqf_60790/09_2025/9iqf_60790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iqf_60790/09_2025/9iqf_60790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iqf_60790/09_2025/9iqf_60790.cif"
  }
  resolution = 4.01
  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=   0.006 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
     P       2      5.49       5
     S      33      5.16       5
     C    5781      2.51       5
     N    1612      2.21       5
     O    1690      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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9118
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4348
          Classifications: {'peptide': 574}
          Link IDs: {'PTRANS': 19, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 4743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 619, 4743
          Classifications: {'peptide': 619}
          Link IDs: {'PTRANS': 18, 'TRANS': 600}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.01, per 1000 atoms: 0.22
  Number of scatterers: 9118
  At special positions: 0
  Unit cell: (71.552, 90.688, 148.928, 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)
     S      33     16.00
     P       2     15.00
     O    1690      8.00
     N    1612      7.00
     C    5781      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 336.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2194

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 5 sheets defined
      72.8% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 0 through 10
    Processing helix  chain 'A' and resid 13 through 49
      removed outlier: 3.572A  pdb=" N   ALA A  18 " --> pdb=" O   ARG A  14 " (cutoff:3.500A)
      removed outlier: 4.832A  pdb=" N   VAL A  19 " --> pdb=" O   TRP A  15 " (cutoff:3.500A)
      Proline residue:  A  35  - end of helix
      removed outlier: 3.631A  pdb=" N   ILE A  42 " --> pdb=" O   ASN A  38 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A  46 " --> pdb=" O   ILE A  42 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   ALA A  47 " --> pdb=" O   ASP A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 100
      removed outlier: 3.762A  pdb=" N   THR A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 110
    Processing helix  chain 'A' and resid 110 through 120
    Processing helix  chain 'A' and resid 120 through 135
    Processing helix  chain 'A' and resid 137 through 154
    Processing helix  chain 'A' and resid 157 through 204
      removed outlier: 3.924A  pdb=" N   LEU A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      Proline residue:  A 166  - end of helix
      removed outlier: 3.530A  pdb=" N   HIS A 178 " --> pdb=" O   TRP A 174 " (cutoff:3.500A)
      Proline residue:  A 181  - end of helix
    Processing helix  chain 'A' and resid 204 through 211
    Processing helix  chain 'A' and resid 212 through 266
      removed outlier: 3.719A  pdb=" N   TRP A 237 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   LEU A 242 " --> pdb=" O   GLN A 238 " (cutoff:3.500A)
      Proline residue:  A 243  - end of helix
      removed outlier: 3.851A  pdb=" N   LEU A 262 " --> pdb=" O   TRP A 258 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 295
      removed outlier: 3.840A  pdb=" N   ILE A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 314
      removed outlier: 3.790A  pdb=" N   THR A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 382
      removed outlier: 3.617A  pdb=" N   LEU A 377 " --> pdb=" O   GLY A 373 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ILE A 378 " --> pdb=" O   LYS A 374 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   SER A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 402
      No H-bonds generated for 'chain 'A' and resid 400 through 402'
    Processing helix  chain 'A' and resid 403 through 410
    Processing helix  chain 'A' and resid 425 through 429
    Processing helix  chain 'A' and resid 430 through 433
    Processing helix  chain 'A' and resid 437 through 448
    Processing helix  chain 'A' and resid 450 through 457
      removed outlier: 3.624A  pdb=" N   VAL A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 474 through 488
      removed outlier: 4.021A  pdb=" N   GLN A 478 " --> pdb=" O   GLY A 474 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ARG A 488 " --> pdb=" O   ARG A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 518
    Processing helix  chain 'A' and resid 529 through 533
    Processing helix  chain 'A' and resid 552 through 560
      removed outlier: 4.472A  pdb=" N   ALA A 558 " --> pdb=" O   ASP A 554 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 571
      removed outlier: 3.849A  pdb=" N   PHE A 566 " --> pdb=" O   ILE A 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 27
    Processing helix  chain 'B' and resid 28 through 31
    Processing helix  chain 'B' and resid 32 through 69
      Proline residue:  B  53  - end of helix
    Processing helix  chain 'B' and resid 77 through 88
      removed outlier: 3.693A  pdb=" N   ARG B  88 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 100
    Processing helix  chain 'B' and resid 109 through 160
    Processing helix  chain 'B' and resid 161 through 167
      removed outlier: 4.057A  pdb=" N   PHE B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 178
      removed outlier: 4.030A  pdb=" N   VAL B 173 " --> pdb=" O   GLN B 169 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU B 174 " --> pdb=" O   ARG B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 213
      removed outlier: 4.329A  pdb=" N   MET B 190 " --> pdb=" O   ASN B 186 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   LEU B 196 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
    Processing helix  chain 'B' and resid 222 through 262
      removed outlier: 3.681A  pdb=" N   ALA B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      Proline residue:  B 240  - end of helix
      removed outlier: 3.771A  pdb=" N   GLY B 262 " --> pdb=" O   GLU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 268
    Processing helix  chain 'B' and resid 271 through 299
    Processing helix  chain 'B' and resid 299 through 326
      removed outlier: 3.713A  pdb=" N   ALA B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 348
      removed outlier: 3.638A  pdb=" N   ARG B 341 " --> pdb=" O   ILE B 337 " (cutoff:3.500A)
      Proline residue:  B 346  - end of helix
    Processing helix  chain 'B' and resid 349 through 372
    Processing helix  chain 'B' and resid 429 through 438
    Processing helix  chain 'B' and resid 456 through 458
      No H-bonds generated for 'chain 'B' and resid 456 through 458'
    Processing helix  chain 'B' and resid 459 through 468
      removed outlier: 3.788A  pdb=" N   SER B 466 " --> pdb=" O   SER B 462 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   GLY B 468 " --> pdb=" O   ARG B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 487
    Processing helix  chain 'B' and resid 493 through 504
    Processing helix  chain 'B' and resid 506 through 511
      removed outlier: 4.112A  pdb=" N   HIS B 511 " --> pdb=" O   ASP B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 544
      removed outlier: 3.774A  pdb=" N   ALA B 544 " --> pdb=" O   ARG B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 571
    Processing helix  chain 'B' and resid 585 through 589
    Processing helix  chain 'B' and resid 608 through 615
    Processing helix  chain 'B' and resid 617 through 629
      removed outlier: 3.544A  pdb=" N   LEU B 627 " --> pdb=" O   THR B 623 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 356
      removed outlier: 5.721A  pdb=" N   ALA A 339 " --> pdb=" O   ASP A 353 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   SER A 355 " --> pdb=" O   HIS A 337 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   HIS A 337 " --> pdb=" O   SER A 355 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414
      removed outlier: 6.339A  pdb=" N   GLY A 412 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   ASP A 496 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   VAL A 414 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   THR A 363 " --> pdb=" O   GLN A 538 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   VAL A 540 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA A 365 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ILE A 542 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL A 367 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   VAL A 539 " --> pdb=" O   ILE A 550 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ILE A 550 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   VAL A 541 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424
    Processing sheet with id=AA4, first strand: chain 'B' and resid 413 through 414
      removed outlier: 3.629A  pdb=" N   ALA B 414 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 469 through 470
      removed outlier: 6.560A  pdb=" N   VAL B 470 " --> pdb=" O   ASP B 552 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU B 549 " --> pdb=" O   THR B 578 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA B 421 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   MET B 598 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   VAL B 423 " --> pdb=" O   MET B 598 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU B 605 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)

    640 hydrogen bonds defined for protein.
    1860 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: 1.42

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3082
        1.34 -     1.46: 1954
        1.46 -     1.58: 4174
        1.58 -     1.70: 3
        1.70 -     1.81: 61
  Bond restraints: 9274
  Sorted by residual:
  bond pdb=" N   LEU A  34 "
       pdb=" CA  LEU A  34 "
    ideal  model  delta    sigma   weight residual
    1.462  1.483 -0.021 7.70e-03 1.69e+04 7.16e+00
  bond pdb=" N   GLU A 213 "
       pdb=" CA  GLU A 213 "
    ideal  model  delta    sigma   weight residual
    1.462  1.485 -0.023 9.50e-03 1.11e+04 5.94e+00
  bond pdb=" N   ASN A 172 "
       pdb=" CA  ASN A 172 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.19e-02 7.06e+03 5.13e+00
  bond pdb=" N   HIS B 158 "
       pdb=" CA  HIS B 158 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.28e-02 6.10e+03 4.90e+00
  bond pdb=" N   LEU A 168 "
       pdb=" CA  LEU A 168 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.023 1.19e-02 7.06e+03 3.85e+00
  ... (remaining 9269 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 12395
        2.20 -     4.40: 185
        4.40 -     6.60: 39
        6.60 -     8.80: 7
        8.80 -    11.00: 2
  Bond angle restraints: 12628
  Sorted by residual:
  angle pdb=" N   LEU A 168 "
        pdb=" CA  LEU A 168 "
        pdb=" C   LEU A 168 "
      ideal   model   delta    sigma   weight residual
     111.07  106.27    4.80 1.07e+00 8.73e-01 2.01e+01
  angle pdb=" N   VAL A 533 "
        pdb=" CA  VAL A 533 "
        pdb=" C   VAL A 533 "
      ideal   model   delta    sigma   weight residual
     113.53  109.85    3.68 9.80e-01 1.04e+00 1.41e+01
  angle pdb=" CB  MET A  61 "
        pdb=" CG  MET A  61 "
        pdb=" SD  MET A  61 "
      ideal   model   delta    sigma   weight residual
     112.70  123.70  -11.00 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" C   GLU B 257 "
        pdb=" N   GLU B 258 "
        pdb=" CA  GLU B 258 "
      ideal   model   delta    sigma   weight residual
     121.58  114.84    6.74 1.95e+00 2.63e-01 1.19e+01
  angle pdb=" CA  MET A  61 "
        pdb=" CB  MET A  61 "
        pdb=" CG  MET A  61 "
      ideal   model   delta    sigma   weight residual
     114.10  120.65   -6.55 2.00e+00 2.50e-01 1.07e+01
  ... (remaining 12623 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 4992
       17.00 -    34.00: 406
       34.00 -    51.00: 83
       51.00 -    68.00: 21
       68.00 -    85.00: 9
  Dihedral angle restraints: 5511
    sinusoidal: 2102
      harmonic: 3409
  Sorted by residual:
  dihedral pdb=" CA  ILE B 102 "
           pdb=" C   ILE B 102 "
           pdb=" N   VAL B 103 "
           pdb=" CA  VAL B 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.41   17.59     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  ARG A 383 "
           pdb=" C   ARG A 383 "
           pdb=" N   LEU A 384 "
           pdb=" CA  LEU A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.49   16.51     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ASP B 559 "
           pdb=" CB  ASP B 559 "
           pdb=" CG  ASP B 559 "
           pdb=" OD1 ASP B 559 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.21   53.21     1      2.00e+01 2.50e-03 9.63e+00
  ... (remaining 5508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1069
       0.040 -    0.080: 335
       0.080 -    0.120: 93
       0.120 -    0.159: 21
       0.159 -    0.199: 2
  Chirality restraints: 1520
  Sorted by residual:
  chirality pdb=" CB  ILE B 528 "
            pdb=" CA  ILE B 528 "
            pdb=" CG1 ILE B 528 "
            pdb=" CG2 ILE B 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.94e-01
  chirality pdb=" CA  HIS B 158 "
            pdb=" N   HIS B 158 "
            pdb=" C   HIS B 158 "
            pdb=" CB  HIS B 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.34e-01
  chirality pdb=" CA  LEU A 168 "
            pdb=" N   LEU A 168 "
            pdb=" C   LEU A 168 "
            pdb=" CB  LEU A 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.19e-01
  ... (remaining 1517 not shown)

  Planarity restraints: 1617
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 358 "    0.035 5.00e-02 4.00e+02   5.26e-02 4.42e+00
        pdb=" N   PRO A 359 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 359 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 359 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  52 "    0.009 2.00e-02 2.50e+03   1.86e-02 3.46e+00
        pdb=" C   ALA A  52 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ALA A  52 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A  53 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  52 "    0.030 5.00e-02 4.00e+02   4.54e-02 3.29e+00
        pdb=" N   PRO B  53 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B  53 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  53 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1614 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1451
        2.76 -     3.29: 10159
        3.29 -     3.83: 16012
        3.83 -     4.36: 17711
        4.36 -     4.90: 30143
  Nonbonded interactions: 75476
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 214 "
            pdb=" OG1 THR B 217 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   VAL B  50 "
            pdb=" OH  TYR B 339 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG1 THR A  36 "
            pdb=" OH  TYR A 280 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" NH2 ARG A 212 "
            pdb=" O   GLY B 488 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" O   GLY A 203 "
            pdb=" N   ARG A 205 "
     model   vdw
     2.245 3.120
  ... (remaining 75471 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.000
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
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      :  0.003   0.034   9274  Z= 0.151
  Angle     :  0.687  11.002  12628  Z= 0.355
  Chirality :  0.043   0.199   1520
  Planarity :  0.004   0.053   1617
  Dihedral  : 13.690  85.001   3317
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.62 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.63 %
    Favored  : 99.27 %
  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:  1.15 (0.24), residues: 1189
  helix:  1.38 (0.18), residues: 772
  sheet:  0.42 (0.80), residues: 48
  loop : -0.40 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 545 
 TYR   0.013   0.001   TYR A 280 
 PHE   0.024   0.001   PHE B 343 
 TRP   0.010   0.001   TRP A 159 
 HIS   0.003   0.001   HIS B 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9274)
  covalent geometry    : angle       0.68686 (12628)
  hydrogen bonds       : bond        0.12325 (  640)
  hydrogen bonds       : angle       5.06497 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9396 (mp) cc_final: 0.9148 (mp)
REVERT: A  121 ASP cc_start: 0.8053 (m-30) cc_final: 0.7657 (m-30)
REVERT: A  172 ASN cc_start: 0.9109 (m-40) cc_final: 0.8791 (m110)
REVERT: A  250 ASN cc_start: 0.9533 (m110) cc_final: 0.9089 (m-40)
REVERT: A  306 ASP cc_start: 0.8354 (m-30) cc_final: 0.7785 (t0)
REVERT: A  310 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8157 (mt-10)
REVERT: A  318 ILE cc_start: 0.8865 (mm) cc_final: 0.8558 (pt)
REVERT: A  408 TRP cc_start: 0.9158 (m-10) cc_final: 0.8862 (m-10)
REVERT: A  416 GLN cc_start: 0.8488 (pm20) cc_final: 0.8267 (pm20)
REVERT: A  478 GLN cc_start: 0.9439 (mp10) cc_final: 0.8987 (mp10)
REVERT: B  198 SER cc_start: 0.9685 (m) cc_final: 0.9421 (p)
REVERT: B  208 MET cc_start: 0.8682 (tpp) cc_final: 0.8469 (tpp)
REVERT: B  269 PHE cc_start: 0.8780 (m-80) cc_final: 0.8536 (m-80)
REVERT: B  342 GLN cc_start: 0.9069 (mp10) cc_final: 0.8794 (mp10)
REVERT: B  372 ASP cc_start: 0.8569 (m-30) cc_final: 0.8271 (p0)
REVERT: B  423 VAL cc_start: 0.9210 (t) cc_final: 0.8812 (p)
REVERT: B  436 LEU cc_start: 0.9121 (mt) cc_final: 0.8842 (mt)
REVERT: B  480 THR cc_start: 0.8817 (p) cc_final: 0.8370 (p)
REVERT: B  570 MET cc_start: 0.9055 (ppp) cc_final: 0.8693 (mmp)
REVERT: B  612 LEU cc_start: 0.9386 (tp) cc_final: 0.9126 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 196
  average time/residue: 0.0668
  time to fit residues: 19.5757
Evaluate side-chains
  165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:   10.0000
   chunk 117 optimal weight:   10.0000
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 ASN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.067736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.054117 restraints weight = 38128.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.055994 restraints weight = 21679.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.057301 restraints weight = 14512.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.058262 restraints weight = 10732.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.058910 restraints weight = 8511.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.0869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9274  Z= 0.181
  Angle     :  0.642   9.529  12628  Z= 0.330
  Chirality :  0.042   0.165   1520
  Planarity :  0.004   0.052   1617
  Dihedral  :  4.574  31.597   1318
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.95 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  5.22 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.21 (0.24), residues: 1189
  helix:  1.49 (0.18), residues: 783
  sheet: -0.32 (0.71), residues: 60
  loop : -0.48 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 561 
 TYR   0.010   0.001   TYR A   9 
 PHE   0.011   0.001   PHE B 343 
 TRP   0.010   0.001   TRP B 132 
 HIS   0.009   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 9274)
  covalent geometry    : angle       0.64163 (12628)
  hydrogen bonds       : bond        0.04289 (  640)
  hydrogen bonds       : angle       4.51287 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 188
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9425 (mp) cc_final: 0.9170 (mp)
REVERT: A  101 PHE cc_start: 0.9309 (m-10) cc_final: 0.9030 (m-80)
REVERT: A  121 ASP cc_start: 0.8252 (m-30) cc_final: 0.7834 (m-30)
REVERT: A  280 TYR cc_start: 0.9460 (m-10) cc_final: 0.8721 (m-80)
REVERT: A  306 ASP cc_start: 0.8323 (m-30) cc_final: 0.7807 (t0)
REVERT: A  310 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8227 (mt-10)
REVERT: A  478 GLN cc_start: 0.9427 (mp10) cc_final: 0.8999 (mp10)
REVERT: B  129 LEU cc_start: 0.9567 (mt) cc_final: 0.9361 (mt)
REVERT: B  198 SER cc_start: 0.9727 (m) cc_final: 0.9506 (p)
REVERT: B  208 MET cc_start: 0.8697 (tpp) cc_final: 0.8322 (tpp)
REVERT: B  215 LEU cc_start: 0.8826 (mp) cc_final: 0.8473 (tp)
REVERT: B  342 GLN cc_start: 0.9096 (mp10) cc_final: 0.8812 (mp10)
REVERT: B  369 ASP cc_start: 0.8699 (m-30) cc_final: 0.8245 (m-30)
REVERT: B  436 LEU cc_start: 0.9110 (mt) cc_final: 0.8824 (mt)
REVERT: B  442 ASP cc_start: 0.8233 (p0) cc_final: 0.8032 (p0)
REVERT: B  469 MET cc_start: 0.8508 (tmm) cc_final: 0.8307 (tmm)
REVERT: B  480 THR cc_start: 0.8864 (p) cc_final: 0.8581 (p)
REVERT: B  563 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8542 (tm-30)
REVERT: B  570 MET cc_start: 0.9054 (ppp) cc_final: 0.8612 (ppp)
  outliers start: 3
  outliers final: 0
  residues processed: 190
  average time/residue: 0.0706
  time to fit residues: 20.1527
Evaluate side-chains
  146 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   chunk 103 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 73 optimal weight:    0.6980
   chunk 102 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  28 ASN
A 172 ASN
B 344 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.068891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.055103 restraints weight = 37619.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.057031 restraints weight = 21523.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.058379 restraints weight = 14419.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.059347 restraints weight = 10632.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.060032 restraints weight = 8447.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9274  Z= 0.137
  Angle     :  0.623   7.964  12628  Z= 0.313
  Chirality :  0.042   0.231   1520
  Planarity :  0.004   0.055   1617
  Dihedral  :  4.527  31.817   1318
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.36 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  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:  1.16 (0.24), residues: 1189
  helix:  1.49 (0.18), residues: 782
  sheet: -0.28 (0.71), residues: 60
  loop : -0.59 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 511 
 TYR   0.010   0.001   TYR A   9 
 PHE   0.010   0.001   PHE A  77 
 TRP   0.010   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9274)
  covalent geometry    : angle       0.62255 (12628)
  hydrogen bonds       : bond        0.04102 (  640)
  hydrogen bonds       : angle       4.43104 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 187
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9431 (mp) cc_final: 0.9165 (mp)
REVERT: A  101 PHE cc_start: 0.9232 (m-10) cc_final: 0.9006 (m-80)
REVERT: A  120 ASN cc_start: 0.8768 (m110) cc_final: 0.8534 (m110)
REVERT: A  121 ASP cc_start: 0.8250 (m-30) cc_final: 0.7849 (m-30)
REVERT: A  280 TYR cc_start: 0.9398 (m-10) cc_final: 0.8755 (m-80)
REVERT: A  293 PHE cc_start: 0.7458 (t80) cc_final: 0.7214 (t80)
REVERT: A  306 ASP cc_start: 0.8333 (m-30) cc_final: 0.7756 (t0)
REVERT: A  310 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8184 (mt-10)
REVERT: A  478 GLN cc_start: 0.9417 (mp10) cc_final: 0.8982 (mp10)
REVERT: B  194 GLN cc_start: 0.8357 (pt0) cc_final: 0.7575 (pt0)
REVERT: B  198 SER cc_start: 0.9756 (m) cc_final: 0.9478 (p)
REVERT: B  208 MET cc_start: 0.8632 (tpp) cc_final: 0.8314 (tpp)
REVERT: B  215 LEU cc_start: 0.8802 (mp) cc_final: 0.8566 (mm)
REVERT: B  219 PHE cc_start: 0.8916 (m-80) cc_final: 0.8682 (m-80)
REVERT: B  342 GLN cc_start: 0.9040 (mp10) cc_final: 0.8748 (mt0)
REVERT: B  436 LEU cc_start: 0.9087 (mt) cc_final: 0.8788 (mt)
REVERT: B  442 ASP cc_start: 0.8312 (p0) cc_final: 0.8077 (p0)
REVERT: B  469 MET cc_start: 0.8500 (tmm) cc_final: 0.8281 (tmm)
REVERT: B  533 LYS cc_start: 0.9205 (mttm) cc_final: 0.8776 (mmtm)
REVERT: B  563 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8771 (tm-30)
REVERT: B  570 MET cc_start: 0.9052 (ppp) cc_final: 0.8567 (ppp)
  outliers start: 1
  outliers final: 1
  residues processed: 187
  average time/residue: 0.0621
  time to fit residues: 17.5941
Evaluate side-chains
  151 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0770
   chunk 66 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
B 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.069660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.055348 restraints weight = 38089.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.057290 restraints weight = 21918.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.058677 restraints weight = 14802.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.059666 restraints weight = 10959.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.060318 restraints weight = 8727.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9274  Z= 0.127
  Angle     :  0.621   8.005  12628  Z= 0.312
  Chirality :  0.042   0.167   1520
  Planarity :  0.004   0.056   1617
  Dihedral  :  4.544  31.997   1318
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.62 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.03 %
    Favored  : 96.76 %
  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:  1.25 (0.24), residues: 1189
  helix:  1.53 (0.18), residues: 781
  sheet: -0.15 (0.72), residues: 60
  loop : -0.53 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 615 
 TYR   0.009   0.001   TYR A   9 
 PHE   0.035   0.001   PHE A 183 
 TRP   0.010   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9274)
  covalent geometry    : angle       0.62129 (12628)
  hydrogen bonds       : bond        0.03961 (  640)
  hydrogen bonds       : angle       4.38844 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9423 (mp) cc_final: 0.9167 (mp)
REVERT: A  101 PHE cc_start: 0.9222 (m-10) cc_final: 0.8945 (m-80)
REVERT: A  120 ASN cc_start: 0.8750 (m110) cc_final: 0.8523 (m110)
REVERT: A  121 ASP cc_start: 0.8177 (m-30) cc_final: 0.7762 (m-30)
REVERT: A  293 PHE cc_start: 0.7449 (t80) cc_final: 0.7193 (t80)
REVERT: A  306 ASP cc_start: 0.8338 (m-30) cc_final: 0.7801 (t0)
REVERT: A  310 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8177 (mt-10)
REVERT: A  376 THR cc_start: 0.9284 (p) cc_final: 0.9081 (p)
REVERT: A  416 GLN cc_start: 0.8271 (pm20) cc_final: 0.7862 (pm20)
REVERT: A  478 GLN cc_start: 0.9393 (mp10) cc_final: 0.8989 (mp10)
REVERT: A  496 ASP cc_start: 0.8560 (t70) cc_final: 0.7538 (t0)
REVERT: B  194 GLN cc_start: 0.8387 (pt0) cc_final: 0.7617 (pt0)
REVERT: B  208 MET cc_start: 0.8589 (tpp) cc_final: 0.8197 (tpp)
REVERT: B  215 LEU cc_start: 0.8786 (mp) cc_final: 0.8554 (mm)
REVERT: B  219 PHE cc_start: 0.8898 (m-80) cc_final: 0.8679 (m-80)
REVERT: B  342 GLN cc_start: 0.9112 (mp10) cc_final: 0.8856 (mp10)
REVERT: B  369 ASP cc_start: 0.8754 (m-30) cc_final: 0.8331 (m-30)
REVERT: B  436 LEU cc_start: 0.9078 (mt) cc_final: 0.8780 (mt)
REVERT: B  442 ASP cc_start: 0.8385 (p0) cc_final: 0.8185 (p0)
REVERT: B  533 LYS cc_start: 0.9153 (mttm) cc_final: 0.8759 (mmtm)
REVERT: B  563 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8778 (tm-30)
REVERT: B  570 MET cc_start: 0.9004 (ppp) cc_final: 0.8767 (ppp)
  outliers start: 2
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0690
  time to fit residues: 19.6740
Evaluate side-chains
  149 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 115 optimal weight:   20.0000
   chunk 85 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 96 optimal weight:   40.0000
   chunk 27 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.068954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.054633 restraints weight = 38460.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.056548 restraints weight = 22377.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.057898 restraints weight = 15142.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.058842 restraints weight = 11288.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.059493 restraints weight = 9063.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9274  Z= 0.157
  Angle     :  0.624   8.295  12628  Z= 0.317
  Chirality :  0.042   0.162   1520
  Planarity :  0.004   0.055   1617
  Dihedral  :  4.520  33.065   1318
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.70 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  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:  1.28 (0.24), residues: 1189
  helix:  1.56 (0.18), residues: 786
  sheet: -0.36 (0.70), residues: 60
  loop : -0.52 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 212 
 TYR   0.010   0.001   TYR A   9 
 PHE   0.027   0.001   PHE A 183 
 TRP   0.009   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9274)
  covalent geometry    : angle       0.62397 (12628)
  hydrogen bonds       : bond        0.03920 (  640)
  hydrogen bonds       : angle       4.45656 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9450 (mp) cc_final: 0.9198 (mp)
REVERT: A  101 PHE cc_start: 0.9219 (m-10) cc_final: 0.8964 (m-80)
REVERT: A  120 ASN cc_start: 0.8741 (m110) cc_final: 0.8535 (m110)
REVERT: A  121 ASP cc_start: 0.8302 (m-30) cc_final: 0.7863 (m-30)
REVERT: A  250 ASN cc_start: 0.9460 (m-40) cc_final: 0.9031 (t0)
REVERT: A  280 TYR cc_start: 0.9284 (m-10) cc_final: 0.8738 (m-80)
REVERT: A  293 PHE cc_start: 0.7435 (t80) cc_final: 0.7192 (t80)
REVERT: A  306 ASP cc_start: 0.8353 (m-30) cc_final: 0.7808 (t0)
REVERT: A  310 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8199 (mt-10)
REVERT: A  416 GLN cc_start: 0.8265 (pm20) cc_final: 0.7875 (pm20)
REVERT: A  478 GLN cc_start: 0.9425 (mp10) cc_final: 0.9006 (mp10)
REVERT: A  496 ASP cc_start: 0.8580 (t70) cc_final: 0.7519 (t0)
REVERT: B  194 GLN cc_start: 0.8422 (pt0) cc_final: 0.7610 (pt0)
REVERT: B  208 MET cc_start: 0.8587 (tpp) cc_final: 0.8247 (tpp)
REVERT: B  215 LEU cc_start: 0.8822 (mp) cc_final: 0.8567 (mm)
REVERT: B  219 PHE cc_start: 0.8933 (m-80) cc_final: 0.8682 (m-80)
REVERT: B  342 GLN cc_start: 0.9161 (mp10) cc_final: 0.8886 (mp10)
REVERT: B  436 LEU cc_start: 0.9037 (mt) cc_final: 0.8741 (mt)
REVERT: B  442 ASP cc_start: 0.8406 (p0) cc_final: 0.8186 (p0)
REVERT: B  480 THR cc_start: 0.8894 (p) cc_final: 0.8598 (t)
REVERT: B  533 LYS cc_start: 0.9236 (mttm) cc_final: 0.8849 (mmtm)
REVERT: B  563 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8743 (tm-30)
REVERT: B  570 MET cc_start: 0.8998 (ppp) cc_final: 0.8762 (ppp)
  outliers start: 1
  outliers final: 1
  residues processed: 182
  average time/residue: 0.0646
  time to fit residues: 18.0561
Evaluate side-chains
  148 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 109 optimal weight:    0.7980
   chunk 63 optimal weight:   10.0000
   chunk 114 optimal weight:    0.1980
   chunk 35 optimal weight:    0.2980
   chunk 110 optimal weight:    0.0970
   chunk 49 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0670
   chunk 111 optimal weight:    0.9990
   chunk 113 optimal weight:    7.9990
   overall best weight:    0.2916

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

Flipped N/Q/H residues before XYZ refinement:
A  38 ASN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.070884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.056567 restraints weight = 37667.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.058553 restraints weight = 21822.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.059950 restraints weight = 14720.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.060943 restraints weight = 10930.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.061613 restraints weight = 8700.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9274  Z= 0.125
  Angle     :  0.622   8.366  12628  Z= 0.308
  Chirality :  0.042   0.176   1520
  Planarity :  0.004   0.056   1617
  Dihedral  :  4.499  31.754   1318
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.45 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  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:  1.36 (0.25), residues: 1189
  helix:  1.64 (0.18), residues: 789
  sheet: -0.24 (0.71), residues: 60
  loop : -0.58 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  27 
 TYR   0.008   0.001   TYR A   9 
 PHE   0.021   0.001   PHE A 183 
 TRP   0.009   0.001   TRP B 132 
 HIS   0.007   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9274)
  covalent geometry    : angle       0.62213 (12628)
  hydrogen bonds       : bond        0.03858 (  640)
  hydrogen bonds       : angle       4.29209 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9448 (mp) cc_final: 0.9182 (mp)
REVERT: A  101 PHE cc_start: 0.9166 (m-10) cc_final: 0.8915 (m-80)
REVERT: A  120 ASN cc_start: 0.8674 (m110) cc_final: 0.8472 (m110)
REVERT: A  121 ASP cc_start: 0.8157 (m-30) cc_final: 0.7734 (m-30)
REVERT: A  180 MET cc_start: 0.7490 (ttt) cc_final: 0.6989 (ttt)
REVERT: A  250 ASN cc_start: 0.9417 (m-40) cc_final: 0.8965 (t0)
REVERT: A  306 ASP cc_start: 0.8324 (m-30) cc_final: 0.7731 (t0)
REVERT: A  310 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8193 (mt-10)
REVERT: A  416 GLN cc_start: 0.8252 (pm20) cc_final: 0.7880 (pm20)
REVERT: A  478 GLN cc_start: 0.9377 (mp10) cc_final: 0.9054 (mp10)
REVERT: A  496 ASP cc_start: 0.8552 (t70) cc_final: 0.7492 (t0)
REVERT: B  208 MET cc_start: 0.8510 (tpp) cc_final: 0.8105 (tpp)
REVERT: B  215 LEU cc_start: 0.8756 (mp) cc_final: 0.8345 (tt)
REVERT: B  219 PHE cc_start: 0.8902 (m-80) cc_final: 0.8311 (m-80)
REVERT: B  342 GLN cc_start: 0.9099 (mp10) cc_final: 0.8879 (mp10)
REVERT: B  372 ASP cc_start: 0.8542 (m-30) cc_final: 0.8140 (p0)
REVERT: B  436 LEU cc_start: 0.9092 (mt) cc_final: 0.8788 (mt)
REVERT: B  442 ASP cc_start: 0.8379 (p0) cc_final: 0.8163 (p0)
REVERT: B  480 THR cc_start: 0.8809 (p) cc_final: 0.8534 (t)
REVERT: B  533 LYS cc_start: 0.9162 (mttm) cc_final: 0.8759 (mmtm)
REVERT: B  563 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8707 (tm-30)
REVERT: B  570 MET cc_start: 0.9074 (ppp) cc_final: 0.8869 (ppp)
REVERT: B  619 TYR cc_start: 0.9170 (t80) cc_final: 0.8814 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0605
  time to fit residues: 18.0307
Evaluate side-chains
  155 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0970
   chunk 53 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 94 optimal weight:    8.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  28 ASN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.069623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.055649 restraints weight = 37555.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.057565 restraints weight = 21847.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.058901 restraints weight = 14787.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.059891 restraints weight = 11032.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.060566 restraints weight = 8761.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9274  Z= 0.134
  Angle     :  0.629   8.123  12628  Z= 0.317
  Chirality :  0.042   0.196   1520
  Planarity :  0.004   0.056   1617
  Dihedral  :  4.442  31.522   1318
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.62 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.25 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.35 (0.25), residues: 1189
  helix:  1.60 (0.18), residues: 788
  sheet: -0.30 (0.70), residues: 60
  loop : -0.47 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 341 
 TYR   0.009   0.001   TYR A  13 
 PHE   0.017   0.001   PHE A 183 
 TRP   0.009   0.001   TRP B 132 
 HIS   0.007   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9274)
  covalent geometry    : angle       0.62934 (12628)
  hydrogen bonds       : bond        0.03871 (  640)
  hydrogen bonds       : angle       4.39818 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9422 (mp) cc_final: 0.9188 (mp)
REVERT: A  101 PHE cc_start: 0.9206 (m-10) cc_final: 0.8846 (m-80)
REVERT: A  120 ASN cc_start: 0.8710 (m110) cc_final: 0.8484 (m110)
REVERT: A  121 ASP cc_start: 0.8270 (m-30) cc_final: 0.7844 (m-30)
REVERT: A  250 ASN cc_start: 0.9458 (m-40) cc_final: 0.8963 (t0)
REVERT: A  306 ASP cc_start: 0.8391 (m-30) cc_final: 0.8065 (t0)
REVERT: A  416 GLN cc_start: 0.8249 (pm20) cc_final: 0.7854 (pm20)
REVERT: A  478 GLN cc_start: 0.9418 (mp10) cc_final: 0.9009 (mp10)
REVERT: A  496 ASP cc_start: 0.8549 (t70) cc_final: 0.7479 (t0)
REVERT: B  208 MET cc_start: 0.8544 (tpp) cc_final: 0.8155 (tpp)
REVERT: B  215 LEU cc_start: 0.8784 (mp) cc_final: 0.8369 (tt)
REVERT: B  219 PHE cc_start: 0.8928 (m-80) cc_final: 0.8331 (m-80)
REVERT: B  436 LEU cc_start: 0.9074 (mt) cc_final: 0.8769 (mt)
REVERT: B  442 ASP cc_start: 0.8405 (p0) cc_final: 0.8179 (p0)
REVERT: B  480 THR cc_start: 0.8862 (p) cc_final: 0.8545 (t)
REVERT: B  533 LYS cc_start: 0.9214 (mttm) cc_final: 0.8820 (mmtm)
REVERT: B  563 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8718 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 185
  average time/residue: 0.0630
  time to fit residues: 17.6203
Evaluate side-chains
  150 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 67 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 105 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 104 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  28 ASN
A  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.070535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.056332 restraints weight = 37212.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.058269 restraints weight = 21637.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.059617 restraints weight = 14634.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.060613 restraints weight = 10933.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.061312 restraints weight = 8701.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9274  Z= 0.128
  Angle     :  0.644   8.155  12628  Z= 0.321
  Chirality :  0.042   0.171   1520
  Planarity :  0.004   0.056   1617
  Dihedral  :  4.457  31.040   1318
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.03 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  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:  1.34 (0.25), residues: 1189
  helix:  1.60 (0.18), residues: 787
  sheet: -0.32 (0.71), residues: 60
  loop : -0.47 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 300 
 TYR   0.008   0.001   TYR A   9 
 PHE   0.036   0.001   PHE B  64 
 TRP   0.010   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9274)
  covalent geometry    : angle       0.64353 (12628)
  hydrogen bonds       : bond        0.03877 (  640)
  hydrogen bonds       : angle       4.35476 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9414 (mp) cc_final: 0.9168 (mp)
REVERT: A   29 MET cc_start: 0.9316 (mmm) cc_final: 0.9010 (mmm)
REVERT: A  101 PHE cc_start: 0.9176 (m-10) cc_final: 0.8830 (m-80)
REVERT: A  120 ASN cc_start: 0.8704 (m110) cc_final: 0.8481 (m110)
REVERT: A  121 ASP cc_start: 0.8210 (m-30) cc_final: 0.7768 (m-30)
REVERT: A  250 ASN cc_start: 0.9460 (m-40) cc_final: 0.8943 (t0)
REVERT: A  306 ASP cc_start: 0.8404 (m-30) cc_final: 0.8102 (t0)
REVERT: A  416 GLN cc_start: 0.8241 (pm20) cc_final: 0.7848 (pm20)
REVERT: A  478 GLN cc_start: 0.9394 (mp10) cc_final: 0.9009 (mp10)
REVERT: A  496 ASP cc_start: 0.8549 (t70) cc_final: 0.7464 (t0)
REVERT: B  208 MET cc_start: 0.8505 (tpp) cc_final: 0.8125 (tpp)
REVERT: B  215 LEU cc_start: 0.8737 (mp) cc_final: 0.8316 (tt)
REVERT: B  219 PHE cc_start: 0.8899 (m-80) cc_final: 0.8296 (m-80)
REVERT: B  309 ASN cc_start: 0.9233 (m-40) cc_final: 0.8800 (m-40)
REVERT: B  372 ASP cc_start: 0.8528 (m-30) cc_final: 0.8146 (p0)
REVERT: B  436 LEU cc_start: 0.9027 (mt) cc_final: 0.8720 (mt)
REVERT: B  442 ASP cc_start: 0.8362 (p0) cc_final: 0.8117 (p0)
REVERT: B  480 THR cc_start: 0.8822 (p) cc_final: 0.8539 (t)
REVERT: B  533 LYS cc_start: 0.9208 (mttm) cc_final: 0.8805 (mptt)
REVERT: B  563 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8691 (tm-30)
REVERT: B  570 MET cc_start: 0.9201 (ppp) cc_final: 0.8965 (ppp)
REVERT: B  619 TYR cc_start: 0.9182 (t80) cc_final: 0.8956 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0653
  time to fit residues: 18.9621
Evaluate side-chains
  155 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 57 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0020
   chunk 35 optimal weight:    8.9990
   chunk 69 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 114 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
A  28 ASN
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.070990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.057099 restraints weight = 36951.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.059048 restraints weight = 21474.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.060404 restraints weight = 14458.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.061395 restraints weight = 10735.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.062073 restraints weight = 8507.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9274  Z= 0.126
  Angle     :  0.653   9.011  12628  Z= 0.325
  Chirality :  0.042   0.158   1520
  Planarity :  0.004   0.055   1617
  Dihedral  :  4.441  31.276   1318
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.03 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.52 %
    Favored  : 99.37 %
  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:  1.32 (0.25), residues: 1189
  helix:  1.57 (0.18), residues: 788
  sheet: -0.34 (0.71), residues: 60
  loop : -0.44 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 300 
 TYR   0.007   0.001   TYR B 312 
 PHE   0.018   0.001   PHE B  64 
 TRP   0.012   0.001   TRP B 132 
 HIS   0.007   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9274)
  covalent geometry    : angle       0.65292 (12628)
  hydrogen bonds       : bond        0.03842 (  640)
  hydrogen bonds       : angle       4.35782 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9404 (mp) cc_final: 0.9165 (mp)
REVERT: A   32 LEU cc_start: 0.9509 (mt) cc_final: 0.9226 (mt)
REVERT: A  101 PHE cc_start: 0.9143 (m-10) cc_final: 0.8596 (m-80)
REVERT: A  120 ASN cc_start: 0.8756 (m110) cc_final: 0.8519 (m110)
REVERT: A  121 ASP cc_start: 0.8182 (m-30) cc_final: 0.7731 (m-30)
REVERT: A  127 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8922 (tm-30)
REVERT: A  250 ASN cc_start: 0.9431 (m-40) cc_final: 0.8919 (t0)
REVERT: A  306 ASP cc_start: 0.8372 (m-30) cc_final: 0.8074 (t0)
REVERT: A  416 GLN cc_start: 0.8231 (pm20) cc_final: 0.7854 (pm20)
REVERT: A  478 GLN cc_start: 0.9384 (mp10) cc_final: 0.9073 (mp10)
REVERT: A  496 ASP cc_start: 0.8548 (t70) cc_final: 0.7473 (t0)
REVERT: A  505 HIS cc_start: 0.8211 (t-170) cc_final: 0.7942 (t70)
REVERT: B   27 ARG cc_start: 0.8495 (mmt180) cc_final: 0.7873 (mmt180)
REVERT: B   61 ASP cc_start: 0.8893 (t70) cc_final: 0.8662 (t0)
REVERT: B  208 MET cc_start: 0.8499 (tpp) cc_final: 0.8171 (tpp)
REVERT: B  215 LEU cc_start: 0.8710 (mp) cc_final: 0.8271 (tt)
REVERT: B  219 PHE cc_start: 0.8886 (m-80) cc_final: 0.8276 (m-80)
REVERT: B  267 LYS cc_start: 0.9266 (mmmm) cc_final: 0.8929 (tppp)
REVERT: B  309 ASN cc_start: 0.9202 (m-40) cc_final: 0.8755 (m-40)
REVERT: B  372 ASP cc_start: 0.8513 (m-30) cc_final: 0.8125 (p0)
REVERT: B  436 LEU cc_start: 0.8998 (mt) cc_final: 0.8688 (mt)
REVERT: B  442 ASP cc_start: 0.8324 (p0) cc_final: 0.8100 (p0)
REVERT: B  480 THR cc_start: 0.8810 (p) cc_final: 0.8509 (t)
REVERT: B  533 LYS cc_start: 0.9207 (mttm) cc_final: 0.8828 (mptt)
REVERT: B  563 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8691 (tm-30)
REVERT: B  570 MET cc_start: 0.9193 (ppp) cc_final: 0.8639 (ppp)
REVERT: B  619 TYR cc_start: 0.9241 (t80) cc_final: 0.8809 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0663
  time to fit residues: 19.6149
Evaluate side-chains
  162 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 96 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 107 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
B 344 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.070148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.055747 restraints weight = 37531.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.057678 restraints weight = 22243.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.058940 restraints weight = 15139.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.059950 restraints weight = 11550.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.060639 restraints weight = 9229.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9274  Z= 0.159
  Angle     :  0.661   9.053  12628  Z= 0.333
  Chirality :  0.043   0.196   1520
  Planarity :  0.004   0.056   1617
  Dihedral  :  4.449  31.046   1318
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.20 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.42 %
    Favored  : 99.48 %
  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:  1.39 (0.25), residues: 1189
  helix:  1.63 (0.18), residues: 786
  sheet: -0.56 (0.68), residues: 60
  loop : -0.38 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 300 
 TYR   0.011   0.001   TYR A   9 
 PHE   0.024   0.001   PHE B  64 
 TRP   0.011   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9274)
  covalent geometry    : angle       0.66063 (12628)
  hydrogen bonds       : bond        0.03844 (  640)
  hydrogen bonds       : angle       4.39393 ( 1860)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9408 (mp) cc_final: 0.9167 (mp)
REVERT: A  101 PHE cc_start: 0.9195 (m-10) cc_final: 0.8666 (m-80)
REVERT: A  120 ASN cc_start: 0.8798 (m110) cc_final: 0.8554 (m110)
REVERT: A  121 ASP cc_start: 0.8313 (m-30) cc_final: 0.7834 (m-30)
REVERT: A  250 ASN cc_start: 0.9494 (m-40) cc_final: 0.9263 (m-40)
REVERT: A  293 PHE cc_start: 0.7594 (t80) cc_final: 0.7232 (t80)
REVERT: A  306 ASP cc_start: 0.8401 (m-30) cc_final: 0.8108 (t0)
REVERT: A  416 GLN cc_start: 0.8283 (pm20) cc_final: 0.7876 (pm20)
REVERT: A  478 GLN cc_start: 0.9411 (mp10) cc_final: 0.9049 (mp10)
REVERT: A  496 ASP cc_start: 0.8545 (t70) cc_final: 0.7392 (t0)
REVERT: B   27 ARG cc_start: 0.8484 (mmt180) cc_final: 0.7887 (mmt180)
REVERT: B   61 ASP cc_start: 0.8947 (t70) cc_final: 0.8725 (t0)
REVERT: B  208 MET cc_start: 0.8561 (tpp) cc_final: 0.8178 (tpp)
REVERT: B  215 LEU cc_start: 0.8716 (mp) cc_final: 0.8304 (tt)
REVERT: B  219 PHE cc_start: 0.8906 (m-80) cc_final: 0.8318 (m-80)
REVERT: B  267 LYS cc_start: 0.9301 (mmmm) cc_final: 0.8948 (tppp)
REVERT: B  436 LEU cc_start: 0.9035 (mt) cc_final: 0.8731 (mt)
REVERT: B  442 ASP cc_start: 0.8392 (p0) cc_final: 0.8169 (p0)
REVERT: B  480 THR cc_start: 0.8828 (p) cc_final: 0.8516 (t)
REVERT: B  533 LYS cc_start: 0.9262 (mttm) cc_final: 0.8876 (mmtm)
REVERT: B  563 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8717 (tm-30)
REVERT: B  570 MET cc_start: 0.9199 (ppp) cc_final: 0.8618 (ppp)
REVERT: B  619 TYR cc_start: 0.9230 (t80) cc_final: 0.8776 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 185
  average time/residue: 0.0663
  time to fit residues: 18.5845
Evaluate side-chains
  150 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 110 optimal weight:    0.2980
   chunk 96 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 37 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  28 ASN
A  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.070639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.056366 restraints weight = 37069.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.058286 restraints weight = 21715.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.059659 restraints weight = 14792.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.060604 restraints weight = 11055.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.061312 restraints weight = 8885.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9274  Z= 0.132
  Angle     :  0.666   8.878  12628  Z= 0.334
  Chirality :  0.043   0.172   1520
  Planarity :  0.004   0.057   1617
  Dihedral  :  4.474  31.114   1318
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.94 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.31 %
    Favored  : 99.58 %
  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:  1.35 (0.25), residues: 1189
  helix:  1.59 (0.18), residues: 792
  sheet: -0.48 (0.68), residues: 60
  loop : -0.42 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.000   ARG A 489 
 TYR   0.008   0.001   TYR A   9 
 PHE   0.026   0.001   PHE B 242 
 TRP   0.012   0.001   TRP B 132 
 HIS   0.007   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9274)
  covalent geometry    : angle       0.66646 (12628)
  hydrogen bonds       : bond        0.03912 (  640)
  hydrogen bonds       : angle       4.37595 ( 1860)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1405.18 seconds
wall clock time: 25 minutes 2.53 seconds (1502.53 seconds total)