Starting phenix.real_space_refine
on Sun Jun  8 01:30:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iqf_60790/06_2025/9iqf_60790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iqf_60790/06_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_60790/06_2025/9iqf_60790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iqf_60790/06_2025/9iqf_60790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iqf_60790/06_2025/9iqf_60790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iqf_60790/06_2025/9iqf_60790.cif"
  }
  resolution = 4.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.79, per 1000 atoms: 0.85
  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: 2.87
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 0.98
  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: 3.48

  Time building geometry restraints manager: 3.40 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             67.620
  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:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     30.970
  Find NCS groups from input model:        0.160
  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:             0.010
  Load rotamer database and sin/cos tables:3.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  102.840
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (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
 TRP   0.010   0.001   TRP A 159 
 HIS   0.003   0.001   HIS B 271 
 PHE   0.024   0.001   PHE B 343 
 TYR   0.013   0.001   TYR A 280 
 ARG   0.002   0.000   ARG B 545 

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

*********************** 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  : 1.027 
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: 0.1924
  time to fit residues: 55.6900
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  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0370
   chunk 30 optimal weight:   10.0000
   chunk 60 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 92 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0050
   chunk 56 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    0.5074

-------------------------------------------------------------------------------
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**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.070229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.056237 restraints weight = 37176.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.058180 restraints weight = 21378.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.059579 restraints weight = 14391.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.0801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9274  Z= 0.128
  Angle     :  0.624   9.289  12628  Z= 0.314
  Chirality :  0.041   0.159   1520
  Planarity :  0.004   0.050   1617
  Dihedral  :  4.512  29.948   1318
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.28 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.87 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.24), residues: 1189
  helix:  1.49 (0.18), residues: 784
  sheet: -0.11 (0.72), residues: 60
  loop : -0.48 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.009   0.001   HIS B 158 
 PHE   0.010   0.001   PHE A  77 
 TYR   0.010   0.001   TYR A 280 
 ARG   0.003   0.000   ARG B 561 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04285 (  640)
  hydrogen bonds       : angle       4.36292 ( 1860)
  covalent geometry    : bond        0.00257 ( 9274)
  covalent geometry    : angle       0.62428 (12628)

*********************** 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
  204 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 201
  time to evaluate  : 1.636 
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: 0.9393 (mp) cc_final: 0.9154 (mp)
REVERT: A   28 ASN cc_start: 0.8901 (m-40) cc_final: 0.8691 (m-40)
REVERT: A  120 ASN cc_start: 0.8859 (m110) cc_final: 0.8597 (m-40)
REVERT: A  121 ASP cc_start: 0.8112 (m-30) cc_final: 0.7762 (m-30)
REVERT: A  250 ASN cc_start: 0.9427 (m110) cc_final: 0.9118 (m-40)
REVERT: A  306 ASP cc_start: 0.8337 (m-30) cc_final: 0.7754 (t0)
REVERT: A  310 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8222 (mt-10)
REVERT: A  318 ILE cc_start: 0.8875 (mm) cc_final: 0.8552 (pt)
REVERT: A  408 TRP cc_start: 0.9148 (m-10) cc_final: 0.8862 (m-10)
REVERT: A  416 GLN cc_start: 0.8348 (pm20) cc_final: 0.7952 (pm20)
REVERT: A  478 GLN cc_start: 0.9382 (mp10) cc_final: 0.9047 (mp10)
REVERT: A  496 ASP cc_start: 0.8459 (t70) cc_final: 0.7564 (t0)
REVERT: B  198 SER cc_start: 0.9685 (m) cc_final: 0.9454 (p)
REVERT: B  208 MET cc_start: 0.8658 (tpp) cc_final: 0.8357 (tpp)
REVERT: B  215 LEU cc_start: 0.8751 (mp) cc_final: 0.8457 (tp)
REVERT: B  330 LEU cc_start: 0.9180 (tt) cc_final: 0.8943 (tt)
REVERT: B  342 GLN cc_start: 0.9061 (mp10) cc_final: 0.8795 (mp10)
REVERT: B  372 ASP cc_start: 0.8616 (m-30) cc_final: 0.8307 (p0)
REVERT: B  436 LEU cc_start: 0.9099 (mt) cc_final: 0.8825 (mt)
REVERT: B  480 THR cc_start: 0.8833 (p) cc_final: 0.8497 (t)
REVERT: B  563 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8540 (tm-30)
REVERT: B  570 MET cc_start: 0.9046 (ppp) cc_final: 0.8699 (tmm)
REVERT: B  588 THR cc_start: 0.9228 (p) cc_final: 0.9020 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2067
  time to fit residues: 63.6708
Evaluate side-chains
  165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 93 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.7386

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.069590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.055480 restraints weight = 37910.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.057428 restraints weight = 21871.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.058793 restraints weight = 14760.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9274  Z= 0.143
  Angle     :  0.613   7.947  12628  Z= 0.310
  Chirality :  0.042   0.240   1520
  Planarity :  0.004   0.054   1617
  Dihedral  :  4.465  31.218   1318
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.28 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.08 %
    Favored  : 95.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.24), residues: 1189
  helix:  1.54 (0.18), residues: 779
  sheet: -0.18 (0.71), residues: 60
  loop : -0.57 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 
 PHE   0.010   0.001   PHE A  77 
 TYR   0.009   0.001   TYR A   9 
 ARG   0.004   0.000   ARG A 515 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04035 (  640)
  hydrogen bonds       : angle       4.38764 ( 1860)
  covalent geometry    : bond        0.00303 ( 9274)
  covalent geometry    : angle       0.61302 (12628)

*********************** 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
  193 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 191
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9420 (mp) cc_final: 0.9171 (mp)
REVERT: A   28 ASN cc_start: 0.8969 (m-40) cc_final: 0.8748 (m-40)
REVERT: A   62 LEU cc_start: 0.9400 (mt) cc_final: 0.9192 (mt)
REVERT: A  101 PHE cc_start: 0.9302 (m-10) cc_final: 0.9019 (m-80)
REVERT: A  120 ASN cc_start: 0.8847 (m110) cc_final: 0.8614 (m110)
REVERT: A  121 ASP cc_start: 0.8205 (m-30) cc_final: 0.7843 (m-30)
REVERT: A  142 MET cc_start: 0.9535 (mmm) cc_final: 0.9027 (tpt)
REVERT: A  250 ASN cc_start: 0.9474 (m110) cc_final: 0.9117 (m-40)
REVERT: A  293 PHE cc_start: 0.7519 (t80) cc_final: 0.7289 (t80)
REVERT: A  306 ASP cc_start: 0.8401 (m-30) cc_final: 0.7802 (t0)
REVERT: A  310 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8237 (mt-10)
REVERT: A  478 GLN cc_start: 0.9402 (mp10) cc_final: 0.8981 (mp10)
REVERT: B  194 GLN cc_start: 0.8421 (pt0) cc_final: 0.7679 (pt0)
REVERT: B  198 SER cc_start: 0.9715 (m) cc_final: 0.9482 (p)
REVERT: B  208 MET cc_start: 0.8702 (tpp) cc_final: 0.8368 (tpp)
REVERT: B  215 LEU cc_start: 0.8811 (mp) cc_final: 0.8408 (tt)
REVERT: B  219 PHE cc_start: 0.8952 (m-80) cc_final: 0.8340 (m-80)
REVERT: B  372 ASP cc_start: 0.8614 (m-30) cc_final: 0.8296 (p0)
REVERT: B  436 LEU cc_start: 0.9110 (mt) cc_final: 0.8826 (mt)
REVERT: B  533 LYS cc_start: 0.9210 (mttm) cc_final: 0.8787 (mmtm)
REVERT: B  563 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8771 (tm-30)
REVERT: B  570 MET cc_start: 0.9055 (ppp) cc_final: 0.8811 (ppp)
REVERT: B  619 TYR cc_start: 0.9122 (t80) cc_final: 0.8902 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 192
  average time/residue: 0.1645
  time to fit residues: 47.5646
Evaluate side-chains
  158 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 93 optimal weight:    0.0670
   chunk 65 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0370
   chunk 103 optimal weight:    4.9990
   overall best weight:    1.8202

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.069077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.054948 restraints weight = 37729.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.056860 restraints weight = 21957.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.058202 restraints weight = 14856.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9274  Z= 0.146
  Angle     :  0.626   8.240  12628  Z= 0.316
  Chirality :  0.042   0.207   1520
  Planarity :  0.004   0.056   1617
  Dihedral  :  4.483  31.441   1318
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.62 %
    Favored  : 96.30 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.24), residues: 1189
  helix:  1.53 (0.18), residues: 783
  sheet: -0.27 (0.71), residues: 60
  loop : -0.54 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 
 PHE   0.035   0.001   PHE A 183 
 TYR   0.009   0.001   TYR A   9 
 ARG   0.002   0.000   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03947 (  640)
  hydrogen bonds       : angle       4.41590 ( 1860)
  covalent geometry    : bond        0.00313 ( 9274)
  covalent geometry    : angle       0.62638 (12628)

*********************** 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
  193 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9432 (mp) cc_final: 0.9179 (mp)
REVERT: A   62 LEU cc_start: 0.9402 (mt) cc_final: 0.9191 (mt)
REVERT: A  101 PHE cc_start: 0.9226 (m-10) cc_final: 0.9015 (m-80)
REVERT: A  120 ASN cc_start: 0.8840 (m110) cc_final: 0.8583 (m110)
REVERT: A  121 ASP cc_start: 0.8199 (m-30) cc_final: 0.7831 (m-30)
REVERT: A  172 ASN cc_start: 0.9061 (m110) cc_final: 0.8817 (m110)
REVERT: A  250 ASN cc_start: 0.9473 (m110) cc_final: 0.9115 (m-40)
REVERT: A  280 TYR cc_start: 0.9426 (m-10) cc_final: 0.8705 (m-80)
REVERT: A  293 PHE cc_start: 0.7491 (t80) cc_final: 0.7273 (t80)
REVERT: A  306 ASP cc_start: 0.8450 (m-30) cc_final: 0.7849 (t0)
REVERT: A  310 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8293 (mt-10)
REVERT: A  376 THR cc_start: 0.9314 (p) cc_final: 0.9109 (p)
REVERT: A  416 GLN cc_start: 0.8337 (pm20) cc_final: 0.7940 (pm20)
REVERT: A  478 GLN cc_start: 0.9397 (mp10) cc_final: 0.8998 (mp10)
REVERT: A  496 ASP cc_start: 0.8588 (t70) cc_final: 0.7567 (t0)
REVERT: B  194 GLN cc_start: 0.8406 (pt0) cc_final: 0.7702 (pt0)
REVERT: B  198 SER cc_start: 0.9707 (m) cc_final: 0.9445 (p)
REVERT: B  208 MET cc_start: 0.8667 (tpp) cc_final: 0.8272 (tpp)
REVERT: B  215 LEU cc_start: 0.8802 (mp) cc_final: 0.8425 (tt)
REVERT: B  219 PHE cc_start: 0.8939 (m-80) cc_final: 0.8399 (m-80)
REVERT: B  342 GLN cc_start: 0.9180 (mp10) cc_final: 0.8874 (mp10)
REVERT: B  372 ASP cc_start: 0.8627 (m-30) cc_final: 0.8232 (p0)
REVERT: B  436 LEU cc_start: 0.9113 (mt) cc_final: 0.8830 (mt)
REVERT: B  533 LYS cc_start: 0.9188 (mttm) cc_final: 0.8792 (mmtm)
REVERT: B  563 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8769 (tm-30)
REVERT: B  570 MET cc_start: 0.8997 (ppp) cc_final: 0.8768 (ppp)
REVERT: B  619 TYR cc_start: 0.9162 (t80) cc_final: 0.8773 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1905
  time to fit residues: 55.9939
Evaluate side-chains
  158 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 104 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 62 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 70 optimal weight:    0.7980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B 294 GLN
B 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.069241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.055482 restraints weight = 37553.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.057377 restraints weight = 21647.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.058692 restraints weight = 14548.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9274  Z= 0.131
  Angle     :  0.626   8.517  12628  Z= 0.313
  Chirality :  0.042   0.157   1520
  Planarity :  0.004   0.056   1617
  Dihedral  :  4.474  31.507   1318
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.36 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.45 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.24), residues: 1189
  helix:  1.51 (0.18), residues: 785
  sheet: -0.20 (0.72), residues: 60
  loop : -0.54 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 
 PHE   0.030   0.001   PHE A 183 
 TYR   0.009   0.001   TYR A   9 
 ARG   0.003   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (  640)
  hydrogen bonds       : angle       4.36942 ( 1860)
  covalent geometry    : bond        0.00280 ( 9274)
  covalent geometry    : angle       0.62606 (12628)

*********************** 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
  196 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 194
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9434 (mp) cc_final: 0.9174 (mp)
REVERT: A  101 PHE cc_start: 0.9211 (m-10) cc_final: 0.8805 (m-80)
REVERT: A  120 ASN cc_start: 0.8812 (m110) cc_final: 0.8579 (m110)
REVERT: A  121 ASP cc_start: 0.8188 (m-30) cc_final: 0.7813 (m-30)
REVERT: A  293 PHE cc_start: 0.7458 (t80) cc_final: 0.7230 (t80)
REVERT: A  306 ASP cc_start: 0.8428 (m-30) cc_final: 0.7843 (t0)
REVERT: A  310 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8271 (mt-10)
REVERT: A  416 GLN cc_start: 0.8295 (pm20) cc_final: 0.7901 (pm20)
REVERT: A  478 GLN cc_start: 0.9403 (mp10) cc_final: 0.8995 (mp10)
REVERT: A  496 ASP cc_start: 0.8558 (t70) cc_final: 0.7508 (t0)
REVERT: B  194 GLN cc_start: 0.8378 (pt0) cc_final: 0.7684 (pt0)
REVERT: B  198 SER cc_start: 0.9722 (m) cc_final: 0.9497 (p)
REVERT: B  208 MET cc_start: 0.8633 (tpp) cc_final: 0.8237 (tpp)
REVERT: B  215 LEU cc_start: 0.8800 (mp) cc_final: 0.8383 (tt)
REVERT: B  219 PHE cc_start: 0.8946 (m-80) cc_final: 0.8355 (m-80)
REVERT: B  267 LYS cc_start: 0.9259 (mmmm) cc_final: 0.8981 (tppp)
REVERT: B  342 GLN cc_start: 0.9154 (mp10) cc_final: 0.8850 (mp10)
REVERT: B  372 ASP cc_start: 0.8615 (m-30) cc_final: 0.8213 (p0)
REVERT: B  436 LEU cc_start: 0.9078 (mt) cc_final: 0.8793 (mt)
REVERT: B  533 LYS cc_start: 0.9195 (mttm) cc_final: 0.8793 (mmtm)
REVERT: B  563 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8742 (tm-30)
REVERT: B  570 MET cc_start: 0.8982 (ppp) cc_final: 0.8768 (ppp)
  outliers start: 2
  outliers final: 1
  residues processed: 195
  average time/residue: 0.1739
  time to fit residues: 51.7055
Evaluate side-chains
  152 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0570
   chunk 2 optimal weight:    0.9990
   chunk 96 optimal weight:   40.0000
   chunk 98 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.4106

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

Flipped N/Q/H residues before XYZ refinement:
B 294 GLN
** B 322 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 = 0.3283 r_free = 0.3283 target = 0.069660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.055516 restraints weight = 37237.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.057428 restraints weight = 21699.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.058650 restraints weight = 14744.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1550

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= 0.135
  Angle     :  0.622   8.197  12628  Z= 0.313
  Chirality :  0.042   0.183   1520
  Planarity :  0.004   0.055   1617
  Dihedral  :  4.464  30.991   1318
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.53 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.24 %
    Favored  : 96.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.24), residues: 1189
  helix:  1.57 (0.18), residues: 781
  sheet: -0.28 (0.70), residues: 60
  loop : -0.46 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 
 PHE   0.023   0.001   PHE A 183 
 TYR   0.009   0.001   TYR A   9 
 ARG   0.003   0.000   ARG B 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  640)
  hydrogen bonds       : angle       4.37754 ( 1860)
  covalent geometry    : bond        0.00291 ( 9274)
  covalent geometry    : angle       0.62165 (12628)

*********************** 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
  192 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 1.088 
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: 0.9430 (mp) cc_final: 0.9169 (mp)
REVERT: A  101 PHE cc_start: 0.9220 (m-10) cc_final: 0.8808 (m-80)
REVERT: A  120 ASN cc_start: 0.8799 (m110) cc_final: 0.8570 (m110)
REVERT: A  121 ASP cc_start: 0.8273 (m-30) cc_final: 0.7878 (m-30)
REVERT: A  306 ASP cc_start: 0.8431 (m-30) cc_final: 0.7858 (t0)
REVERT: A  310 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8305 (mt-10)
REVERT: A  416 GLN cc_start: 0.8299 (pm20) cc_final: 0.7896 (pm20)
REVERT: A  478 GLN cc_start: 0.9424 (mp10) cc_final: 0.9008 (mp10)
REVERT: A  496 ASP cc_start: 0.8572 (t70) cc_final: 0.7501 (t0)
REVERT: B  198 SER cc_start: 0.9731 (m) cc_final: 0.9454 (p)
REVERT: B  208 MET cc_start: 0.8595 (tpp) cc_final: 0.8184 (tpp)
REVERT: B  215 LEU cc_start: 0.8755 (mp) cc_final: 0.8347 (tt)
REVERT: B  219 PHE cc_start: 0.8950 (m-80) cc_final: 0.8312 (m-80)
REVERT: B  267 LYS cc_start: 0.9297 (mmmm) cc_final: 0.8946 (tppp)
REVERT: B  372 ASP cc_start: 0.8642 (m-30) cc_final: 0.8207 (p0)
REVERT: B  436 LEU cc_start: 0.9081 (mt) cc_final: 0.8783 (mt)
REVERT: B  533 LYS cc_start: 0.9217 (mttm) cc_final: 0.8809 (mmtm)
REVERT: B  563 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8715 (tm-30)
REVERT: B  570 MET cc_start: 0.9081 (ppp) cc_final: 0.8869 (ppp)
REVERT: B  619 TYR cc_start: 0.9218 (t80) cc_final: 0.8952 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 192
  average time/residue: 0.1726
  time to fit residues: 49.8710
Evaluate side-chains
  154 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   chunk 114 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  38 ASN
A 172 ASN
B 322 GLN
B 344 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.068750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.054219 restraints weight = 38383.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.056128 restraints weight = 22386.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.057466 restraints weight = 15219.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9274  Z= 0.175
  Angle     :  0.651   8.221  12628  Z= 0.332
  Chirality :  0.043   0.159   1520
  Planarity :  0.004   0.054   1617
  Dihedral  :  4.492  31.938   1318
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.78 %
    Favored  : 96.13 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.24), residues: 1189
  helix:  1.59 (0.18), residues: 781
  sheet: -0.56 (0.67), residues: 60
  loop : -0.44 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 132 
 HIS   0.007   0.001   HIS B 158 
 PHE   0.017   0.001   PHE A 183 
 TYR   0.013   0.001   TYR A   9 
 ARG   0.003   0.000   ARG B 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  640)
  hydrogen bonds       : angle       4.46204 ( 1860)
  covalent geometry    : bond        0.00373 ( 9274)
  covalent geometry    : angle       0.65124 (12628)

*********************** 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
  178 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9443 (mp) cc_final: 0.9184 (mp)
REVERT: A  101 PHE cc_start: 0.9259 (m-10) cc_final: 0.8765 (m-80)
REVERT: A  120 ASN cc_start: 0.8806 (m110) cc_final: 0.8582 (m110)
REVERT: A  121 ASP cc_start: 0.8433 (m-30) cc_final: 0.7984 (m-30)
REVERT: A  250 ASN cc_start: 0.9467 (m-40) cc_final: 0.9016 (t0)
REVERT: A  293 PHE cc_start: 0.7498 (t80) cc_final: 0.7289 (t80)
REVERT: A  306 ASP cc_start: 0.8428 (m-30) cc_final: 0.7834 (t0)
REVERT: A  310 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8281 (mt-10)
REVERT: A  416 GLN cc_start: 0.8346 (pm20) cc_final: 0.7953 (pm20)
REVERT: A  478 GLN cc_start: 0.9438 (mp10) cc_final: 0.9045 (mp10)
REVERT: A  496 ASP cc_start: 0.8568 (t70) cc_final: 0.7445 (t0)
REVERT: B  198 SER cc_start: 0.9740 (m) cc_final: 0.9488 (p)
REVERT: B  208 MET cc_start: 0.8634 (tpp) cc_final: 0.8289 (tpp)
REVERT: B  215 LEU cc_start: 0.8796 (mp) cc_final: 0.8387 (tt)
REVERT: B  219 PHE cc_start: 0.8974 (m-80) cc_final: 0.8379 (m-80)
REVERT: B  267 LYS cc_start: 0.9329 (mmmm) cc_final: 0.8965 (tppp)
REVERT: B  342 GLN cc_start: 0.9155 (mp10) cc_final: 0.8878 (mp10)
REVERT: B  436 LEU cc_start: 0.9036 (mt) cc_final: 0.8733 (mt)
REVERT: B  533 LYS cc_start: 0.9289 (mttm) cc_final: 0.8897 (mptt)
REVERT: B  563 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8724 (tm-30)
REVERT: B  570 MET cc_start: 0.9057 (ppp) cc_final: 0.8839 (ppp)
  outliers start: 1
  outliers final: 1
  residues processed: 177
  average time/residue: 0.1610
  time to fit residues: 43.3115
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  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 112 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 33 optimal weight:   20.0000
   chunk 81 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.5586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.069405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.054869 restraints weight = 38135.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.056779 restraints weight = 22327.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.058098 restraints weight = 15205.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1725

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= 0.140
  Angle     :  0.640   8.007  12628  Z= 0.322
  Chirality :  0.042   0.147   1520
  Planarity :  0.004   0.055   1617
  Dihedral  :  4.519  31.499   1318
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.87 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.24), residues: 1189
  helix:  1.58 (0.18), residues: 782
  sheet: -0.58 (0.68), residues: 60
  loop : -0.43 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 
 PHE   0.015   0.001   PHE A 183 
 TYR   0.009   0.001   TYR A   9 
 ARG   0.004   0.000   ARG A 515 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  640)
  hydrogen bonds       : angle       4.42270 ( 1860)
  covalent geometry    : bond        0.00302 ( 9274)
  covalent geometry    : angle       0.64021 (12628)

*********************** 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
  190 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 PHE cc_start: 0.9251 (m-10) cc_final: 0.8720 (m-80)
REVERT: A  120 ASN cc_start: 0.8773 (m110) cc_final: 0.8557 (m110)
REVERT: A  121 ASP cc_start: 0.8346 (m-30) cc_final: 0.7885 (m-30)
REVERT: A  142 MET cc_start: 0.9556 (tpp) cc_final: 0.9255 (tpp)
REVERT: A  250 ASN cc_start: 0.9478 (m-40) cc_final: 0.9013 (t0)
REVERT: A  280 TYR cc_start: 0.9357 (m-10) cc_final: 0.8789 (m-80)
REVERT: A  293 PHE cc_start: 0.7404 (t80) cc_final: 0.7097 (t80)
REVERT: A  306 ASP cc_start: 0.8421 (m-30) cc_final: 0.7833 (t0)
REVERT: A  310 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8298 (mt-10)
REVERT: A  416 GLN cc_start: 0.8334 (pm20) cc_final: 0.7930 (pm20)
REVERT: A  478 GLN cc_start: 0.9435 (mp10) cc_final: 0.9047 (mp10)
REVERT: A  496 ASP cc_start: 0.8605 (t70) cc_final: 0.7492 (t0)
REVERT: B  194 GLN cc_start: 0.8375 (pt0) cc_final: 0.7759 (pt0)
REVERT: B  198 SER cc_start: 0.9730 (m) cc_final: 0.9455 (p)
REVERT: B  208 MET cc_start: 0.8599 (tpp) cc_final: 0.8200 (tpp)
REVERT: B  215 LEU cc_start: 0.8770 (mp) cc_final: 0.8356 (tt)
REVERT: B  219 PHE cc_start: 0.8975 (m-80) cc_final: 0.8375 (m-80)
REVERT: B  267 LYS cc_start: 0.9300 (mmmm) cc_final: 0.8887 (tppp)
REVERT: B  342 GLN cc_start: 0.9138 (mp10) cc_final: 0.8879 (mp10)
REVERT: B  436 LEU cc_start: 0.9039 (mt) cc_final: 0.8739 (mt)
REVERT: B  533 LYS cc_start: 0.9260 (mttm) cc_final: 0.8867 (mptt)
REVERT: B  563 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8719 (tm-30)
REVERT: B  570 MET cc_start: 0.9066 (ppp) cc_final: 0.8840 (ppp)
REVERT: B  619 TYR cc_start: 0.9218 (t80) cc_final: 0.8993 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1978
  time to fit residues: 57.8238
Evaluate side-chains
  153 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 99 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 85 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 63 optimal weight:   20.0000
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.6982

-------------------------------------------------------------------------------
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 = 0.3277 r_free = 0.3277 target = 0.068984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.055049 restraints weight = 37332.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.056913 restraints weight = 21811.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.058216 restraints weight = 14809.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.1818

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= 0.145
  Angle     :  0.657   8.785  12628  Z= 0.329
  Chirality :  0.043   0.144   1520
  Planarity :  0.004   0.055   1617
  Dihedral  :  4.500  31.994   1318
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.53 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.94 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.24), residues: 1189
  helix:  1.56 (0.18), residues: 783
  sheet: -0.59 (0.67), residues: 60
  loop : -0.42 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 132 
 HIS   0.007   0.001   HIS B 158 
 PHE   0.014   0.001   PHE A 183 
 TYR   0.016   0.001   TYR A 280 
 ARG   0.004   0.000   ARG A 515 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  640)
  hydrogen bonds       : angle       4.44092 ( 1860)
  covalent geometry    : bond        0.00315 ( 9274)
  covalent geometry    : angle       0.65699 (12628)

*********************** 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
  186 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9488 (mt) cc_final: 0.9201 (mp)
REVERT: A  101 PHE cc_start: 0.9245 (m-10) cc_final: 0.8729 (m-80)
REVERT: A  121 ASP cc_start: 0.8380 (m-30) cc_final: 0.7928 (m-30)
REVERT: A  127 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8985 (tm-30)
REVERT: A  135 MET cc_start: 0.8323 (tpp) cc_final: 0.8122 (mmm)
REVERT: A  142 MET cc_start: 0.9538 (tpp) cc_final: 0.9218 (tpp)
REVERT: A  250 ASN cc_start: 0.9501 (m-40) cc_final: 0.9014 (t0)
REVERT: A  278 LEU cc_start: 0.9679 (mm) cc_final: 0.9340 (mm)
REVERT: A  306 ASP cc_start: 0.8432 (m-30) cc_final: 0.7832 (t0)
REVERT: A  310 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8294 (mt-10)
REVERT: A  416 GLN cc_start: 0.8359 (pm20) cc_final: 0.7932 (pm20)
REVERT: A  478 GLN cc_start: 0.9448 (mp10) cc_final: 0.9059 (mp10)
REVERT: A  496 ASP cc_start: 0.8595 (t70) cc_final: 0.7481 (t0)
REVERT: B  198 SER cc_start: 0.9730 (m) cc_final: 0.9463 (p)
REVERT: B  208 MET cc_start: 0.8608 (tpp) cc_final: 0.8265 (tpp)
REVERT: B  215 LEU cc_start: 0.8780 (mp) cc_final: 0.8359 (tt)
REVERT: B  219 PHE cc_start: 0.8982 (m-80) cc_final: 0.8374 (m-80)
REVERT: B  267 LYS cc_start: 0.9305 (mmmm) cc_final: 0.8915 (tppp)
REVERT: B  342 GLN cc_start: 0.9140 (mp10) cc_final: 0.8881 (mp10)
REVERT: B  436 LEU cc_start: 0.9002 (mt) cc_final: 0.8697 (mt)
REVERT: B  533 LYS cc_start: 0.9258 (mttm) cc_final: 0.8861 (mptt)
REVERT: B  563 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8706 (tm-30)
REVERT: B  570 MET cc_start: 0.9089 (ppp) cc_final: 0.8861 (ppp)
REVERT: B  619 TYR cc_start: 0.9225 (t80) cc_final: 0.8766 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 185
  average time/residue: 0.1636
  time to fit residues: 45.9716
Evaluate side-chains
  156 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   chunk 94 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 117 optimal weight:    0.0010
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.5992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.068919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.054917 restraints weight = 37873.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.056783 restraints weight = 21983.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.058122 restraints weight = 14962.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
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   0.057   9274  Z= 0.146
  Angle     :  0.677   9.003  12628  Z= 0.339
  Chirality :  0.043   0.193   1520
  Planarity :  0.004   0.055   1617
  Dihedral  :  4.538  32.123   1318
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.62 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.24), residues: 1189
  helix:  1.53 (0.18), residues: 782
  sheet: -0.66 (0.66), residues: 60
  loop : -0.40 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 
 PHE   0.033   0.001   PHE B  64 
 TYR   0.016   0.001   TYR A 280 
 ARG   0.002   0.000   ARG B 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03890 (  640)
  hydrogen bonds       : angle       4.45335 ( 1860)
  covalent geometry    : bond        0.00319 ( 9274)
  covalent geometry    : angle       0.67706 (12628)

********************** 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
  189 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9494 (mt) cc_final: 0.9212 (mp)
REVERT: A  101 PHE cc_start: 0.9235 (m-10) cc_final: 0.8726 (m-80)
REVERT: A  121 ASP cc_start: 0.8372 (m-30) cc_final: 0.7906 (m-30)
REVERT: A  142 MET cc_start: 0.9528 (tpp) cc_final: 0.9209 (tpp)
REVERT: A  250 ASN cc_start: 0.9508 (m-40) cc_final: 0.9023 (t0)
REVERT: A  278 LEU cc_start: 0.9687 (mm) cc_final: 0.9286 (mm)
REVERT: A  306 ASP cc_start: 0.8440 (m-30) cc_final: 0.7866 (t0)
REVERT: A  310 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8290 (mt-10)
REVERT: A  416 GLN cc_start: 0.8369 (pm20) cc_final: 0.7933 (pm20)
REVERT: A  478 GLN cc_start: 0.9434 (mp10) cc_final: 0.9116 (mp10)
REVERT: A  496 ASP cc_start: 0.8605 (t70) cc_final: 0.7465 (t0)
REVERT: A  505 HIS cc_start: 0.8267 (t-170) cc_final: 0.7974 (t70)
REVERT: B   27 ARG cc_start: 0.8514 (mmt180) cc_final: 0.7856 (mmt180)
REVERT: B  198 SER cc_start: 0.9722 (m) cc_final: 0.9447 (p)
REVERT: B  208 MET cc_start: 0.8590 (tpp) cc_final: 0.8234 (tpp)
REVERT: B  215 LEU cc_start: 0.8757 (mp) cc_final: 0.8339 (tt)
REVERT: B  219 PHE cc_start: 0.8974 (m-80) cc_final: 0.8365 (m-80)
REVERT: B  267 LYS cc_start: 0.9326 (mmmm) cc_final: 0.8929 (tppp)
REVERT: B  338 GLN cc_start: 0.9198 (mt0) cc_final: 0.8546 (mt0)
REVERT: B  342 GLN cc_start: 0.9132 (mp10) cc_final: 0.8846 (mp10)
REVERT: B  436 LEU cc_start: 0.9070 (mt) cc_final: 0.8730 (mt)
REVERT: B  533 LYS cc_start: 0.9252 (mttm) cc_final: 0.8853 (mmtm)
REVERT: B  563 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8699 (tm-30)
REVERT: B  570 MET cc_start: 0.9080 (ppp) cc_final: 0.8844 (ppp)
REVERT: B  619 TYR cc_start: 0.9272 (t80) cc_final: 0.8834 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1945
  time to fit residues: 55.7129
Evaluate side-chains
  154 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 115 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 112 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3295 r_free = 0.3295 target = 0.069815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.055708 restraints weight = 37106.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.057647 restraints weight = 21662.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.058981 restraints weight = 14650.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2026

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= 0.132
  Angle     :  0.680  12.085  12628  Z= 0.337
  Chirality :  0.044   0.265   1520
  Planarity :  0.004   0.069   1617
  Dihedral  :  4.550  31.462   1318
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.36 %
    Favored  : 96.47 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.25), residues: 1189
  helix:  1.52 (0.18), residues: 780
  sheet: -0.53 (0.68), residues: 60
  loop : -0.38 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 132 
 HIS   0.008   0.001   HIS B 158 
 PHE   0.019   0.001   PHE B  64 
 TYR   0.035   0.001   TYR A 280 
 ARG   0.011   0.000   ARG B 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  640)
  hydrogen bonds       : angle       4.41295 ( 1860)
  covalent geometry    : bond        0.00280 ( 9274)
  covalent geometry    : angle       0.68048 (12628)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3813.89 seconds
wall clock time: 69 minutes 39.71 seconds (4179.71 seconds total)