Starting phenix.real_space_refine
on Thu Mar  6 09:07:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sla_25196/03_2025/7sla_25196_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sla_25196/03_2025/7sla_25196.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sla_25196/03_2025/7sla_25196.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sla_25196/03_2025/7sla_25196.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sla_25196/03_2025/7sla_25196_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sla_25196/03_2025/7sla_25196_neut.cif"
  }
  resolution = 3.15
  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=  -0.002 sd=   0.071
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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    3601      2.51       5
     N     877      2.21       5
     O     943      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5458
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 585, 4512
          Classifications: {'peptide': 585}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 22, 'TRANS': 562}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 911
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.10, per 1000 atoms: 0.75
  Number of scatterers: 5458
  At special positions: 0
  Unit cell: (96.05, 84.15, 111.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O     943      8.00
     N     877      7.00
     C    3601      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 345 " - pdb=" SG  CYS A 351 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 355 " - pdb=" SG  CYS A 361 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 517 " - pdb=" SG  CYS A 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " distance=2.04

  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: 1.26
  Conformation dependent library (CDL) restraints added in 770.9 milliseconds
  

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1290

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 3 sheets defined
      59.4% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 47
    Processing helix  chain 'A' and resid 66 through 76
      removed outlier: 3.911A  pdb=" N   ILE A  70 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A  72 " --> pdb=" O   TRP A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 94
    Processing helix  chain 'A' and resid 96 through 100
      removed outlier: 3.672A  pdb=" N   GLY A  99 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLY A 100 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 96 through 100'
    Processing helix  chain 'A' and resid 101 through 115
      removed outlier: 3.890A  pdb=" N   VAL A 111 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   LEU A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   GLY A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TRP A 114 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 122
    Processing helix  chain 'A' and resid 128 through 136
      removed outlier: 3.506A  pdb=" N   LYS A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 157
      removed outlier: 4.147A  pdb=" N   VAL A 143 " --> pdb=" O   GLN A 139 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 151 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 173
    Processing helix  chain 'A' and resid 177 through 194
      removed outlier: 4.032A  pdb=" N   ILE A 182 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   LEU A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   THR A 194 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 226
      removed outlier: 4.103A  pdb=" N   LEU A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE A 217 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LEU A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   MET A 219 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   HIS A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLU A 225 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 226 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 237
      removed outlier: 3.605A  pdb=" N   MET A 233 " --> pdb=" O   TYR A 229 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   TYR A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   MET A 237 " --> pdb=" O   MET A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 256
      removed outlier: 3.635A  pdb=" N   CYS A 255 " --> pdb=" O   GLN A 252 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   TYR A 256 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 252 through 256'
    Processing helix  chain 'A' and resid 275 through 293
      removed outlier: 3.554A  pdb=" N   ILE A 280 " --> pdb=" O   TRP A 276 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   LEU A 283 " --> pdb=" O   PHE A 279 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   THR A 284 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TRP A 289 " --> pdb=" O   ILE A 285 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   TYR A 290 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   CYS A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 302
    Processing helix  chain 'A' and resid 307 through 321
      removed outlier: 3.961A  pdb=" N   LYS A 311 " --> pdb=" O   MET A 307 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA A 317 " --> pdb=" O   GLY A 313 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLY A 318 " --> pdb=" O   CYS A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 339
      removed outlier: 3.723A  pdb=" N   MET A 333 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 344
    Processing helix  chain 'A' and resid 347 through 356
      removed outlier: 3.728A  pdb=" N   GLU A 352 " --> pdb=" O   PRO A 348 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   LYS A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   TYR A 354 " --> pdb=" O   GLU A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 363
      No H-bonds generated for 'chain 'A' and resid 361 through 363'
    Processing helix  chain 'A' and resid 364 through 372
      removed outlier: 3.736A  pdb=" N   LEU A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL A 371 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 409
      removed outlier: 4.041A  pdb=" N   LEU A 381 " --> pdb=" O   GLY A 377 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU A 383 " --> pdb=" O   ARG A 379 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   SER A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   SER A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LEU A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ASP A 408 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A 409 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 413
    Processing helix  chain 'A' and resid 418 through 428
      removed outlier: 3.594A  pdb=" N   LEU A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 445
      Proline residue:  A 442  - end of helix
      removed outlier: 3.632A  pdb=" N   GLN A 445 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 464
      removed outlier: 3.982A  pdb=" N   TYR A 455 " --> pdb=" O   GLN A 451 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE A 456 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 477
      removed outlier: 4.179A  pdb=" N   ALA A 468 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA A 469 " --> pdb=" O   PRO A 465 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL A 470 " --> pdb=" O   PRO A 466 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TRP A 477 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 507
      removed outlier: 3.734A  pdb=" N   ALA A 485 " --> pdb=" O   ASN A 481 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   PHE A 486 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   TRP A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A 504 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   TYR A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 546
      removed outlier: 4.380A  pdb=" N   ILE A 531 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ILE A 532 " --> pdb=" O   TYR A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 664
      removed outlier: 3.707A  pdb=" N   ALA A 664 " --> pdb=" O   HIS A 660 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 7
      removed outlier: 3.568A  pdb=" N   GLN B   5 " --> pdb=" O   SER B  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 14
      removed outlier: 6.066A  pdb=" N   GLY B  12 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR B  39 " --> pdb=" O   TYR B  96 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   TRP B  38 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL B  50 " --> pdb=" O   TRP B  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 22
      removed outlier: 3.505A  pdb=" N   LEU B  20 " --> pdb=" O   MET B  84 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   MET B  84 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    729 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 827
        1.31 -     1.44: 1570
        1.44 -     1.57: 3136
        1.57 -     1.70: 0
        1.70 -     1.83: 59
  Bond restraints: 5592
  Sorted by residual:
  bond pdb=" C   ILE A 397 "
       pdb=" O   ILE A 397 "
    ideal  model  delta    sigma   weight residual
    1.237  1.187  0.050 1.19e-02 7.06e+03 1.79e+01
  bond pdb=" CA  SER A 393 "
       pdb=" C   SER A 393 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.048 1.27e-02 6.20e+03 1.45e+01
  bond pdb=" N   SER A 393 "
       pdb=" CA  SER A 393 "
    ideal  model  delta    sigma   weight residual
    1.459  1.416  0.043 1.19e-02 7.06e+03 1.31e+01
  bond pdb=" CA  SER B  86 "
       pdb=" C   SER B  86 "
    ideal  model  delta    sigma   weight residual
    1.523  1.476  0.048 1.34e-02 5.57e+03 1.26e+01
  bond pdb=" C   SER A 396 "
       pdb=" O   SER A 396 "
    ideal  model  delta    sigma   weight residual
    1.237  1.195  0.042 1.17e-02 7.31e+03 1.26e+01
  ... (remaining 5587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 7300
        2.14 -     4.28: 242
        4.28 -     6.41: 56
        6.41 -     8.55: 12
        8.55 -    10.69: 5
  Bond angle restraints: 7615
  Sorted by residual:
  angle pdb=" N   CYS A 355 "
        pdb=" CA  CYS A 355 "
        pdb=" C   CYS A 355 "
      ideal   model   delta    sigma   weight residual
     112.88  121.38   -8.50 1.29e+00 6.01e-01 4.34e+01
  angle pdb=" N   PRO A 465 "
        pdb=" CA  PRO A 465 "
        pdb=" C   PRO A 465 "
      ideal   model   delta    sigma   weight residual
     110.70  117.64   -6.94 1.22e+00 6.72e-01 3.24e+01
  angle pdb=" N   SER A  77 "
        pdb=" CA  SER A  77 "
        pdb=" C   SER A  77 "
      ideal   model   delta    sigma   weight residual
     111.07  117.15   -6.08 1.07e+00 8.73e-01 3.23e+01
  angle pdb=" N   LEU B  87 "
        pdb=" CA  LEU B  87 "
        pdb=" C   LEU B  87 "
      ideal   model   delta    sigma   weight residual
     110.50  118.42   -7.92 1.41e+00 5.03e-01 3.15e+01
  angle pdb=" N   ALA A 464 "
        pdb=" CA  ALA A 464 "
        pdb=" C   ALA A 464 "
      ideal   model   delta    sigma   weight residual
     109.81  120.50  -10.69 2.21e+00 2.05e-01 2.34e+01
  ... (remaining 7610 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 2901
       15.94 -    31.88: 318
       31.88 -    47.81: 74
       47.81 -    63.75: 7
       63.75 -    79.69: 6
  Dihedral angle restraints: 3306
    sinusoidal: 1288
      harmonic: 2018
  Sorted by residual:
  dihedral pdb=" CB  CYS A 255 "
           pdb=" SG  CYS A 255 "
           pdb=" SG  CYS A 511 "
           pdb=" CB  CYS A 511 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.85  -66.85     1      1.00e+01 1.00e-02 5.83e+01
  dihedral pdb=" CA  ARG B 106 "
           pdb=" C   ARG B 106 "
           pdb=" N   TYR B 107 "
           pdb=" CA  TYR B 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.17   27.83     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" N   CYS A 355 "
           pdb=" C   CYS A 355 "
           pdb=" CA  CYS A 355 "
           pdb=" CB  CYS A 355 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.15  -12.35     0      2.50e+00 1.60e-01 2.44e+01
  ... (remaining 3303 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 848
       0.122 -    0.243: 43
       0.243 -    0.365: 3
       0.365 -    0.487: 1
       0.487 -    0.608: 1
  Chirality restraints: 896
  Sorted by residual:
  chirality pdb=" CA  CYS A 355 "
            pdb=" N   CYS A 355 "
            pdb=" C   CYS A 355 "
            pdb=" CB  CYS A 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.90    0.61 2.00e-01 2.50e+01 9.25e+00
  chirality pdb=" CA  LYS A 358 "
            pdb=" N   LYS A 358 "
            pdb=" C   LYS A 358 "
            pdb=" CB  LYS A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.58e+00
  chirality pdb=" CA  LEU B  87 "
            pdb=" N   LEU B  87 "
            pdb=" C   LEU B  87 "
            pdb=" CB  LEU B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.32e+00
  ... (remaining 893 not shown)

  Planarity restraints: 923
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 330 "   -0.056 5.00e-02 4.00e+02   8.41e-02 1.13e+01
        pdb=" N   PRO A 331 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 394 "   -0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   LEU A 394 "    0.056 2.00e-02 2.50e+03
        pdb=" O   LEU A 394 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   THR A 395 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 465 "    0.053 5.00e-02 4.00e+02   7.86e-02 9.89e+00
        pdb=" N   PRO A 466 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 466 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 466 "    0.044 5.00e-02 4.00e+02
  ... (remaining 920 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 721
        2.75 -     3.29: 4711
        3.29 -     3.82: 7947
        3.82 -     4.36: 8810
        4.36 -     4.90: 16705
  Nonbonded interactions: 38894
  Sorted by model distance:
  nonbonded pdb=" O   SER B  86 "
            pdb=" OG  SER B  86 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   SER A  64 "
            pdb=" OG  SER A  64 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" O   SER B  58 "
            pdb=" OG  SER B  58 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" ND2 ASN A  25 "
            pdb=" OD1 ASN A 376 "
     model   vdw
     2.371 3.120
  nonbonded pdb=" NH2 ARG A 558 "
            pdb=" O   GLU A 568 "
     model   vdw
     2.375 3.120
  ... (remaining 38889 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.70 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.920
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.095   5592  Z= 0.556
  Angle     :  1.006  10.688   7615  Z= 0.582
  Chirality :  0.065   0.608    896
  Planarity :  0.008   0.084    923
  Dihedral  : 13.721  79.687   2001
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.42 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.31 %
  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: -4.25 (0.25), residues: 694
  helix: -2.22 (0.21), residues: 381
  sheet: -3.16 (0.61), residues: 54
  loop : -3.51 (0.31), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 276 
 HIS   0.005   0.002   HIS A  20 
 PHE   0.026   0.002   PHE A 534 
 TYR   0.012   0.002   TYR A 526 
 ARG   0.006   0.001   ARG A 479 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.580 
Fit side-chains
REVERT: A  192 THR cc_start: 0.8278 (t) cc_final: 0.8012 (p)
REVERT: A  252 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7502 (mm-40)
REVERT: A  254 LYS cc_start: 0.8696 (pttm) cc_final: 0.8240 (ptpp)
REVERT: A  374 MET cc_start: 0.8388 (mmm) cc_final: 0.7879 (mmt)
REVERT: B   35 LYS cc_start: 0.8125 (tttt) cc_final: 0.7657 (tptp)
REVERT: B   70 THR cc_start: 0.8652 (m) cc_final: 0.8290 (p)
  outliers start: 10
  outliers final: 5
  residues processed: 118
  average time/residue: 0.2147
  time to fit residues: 31.4310
Evaluate side-chains
  86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   89 PRO
Chi-restraints excluded: chain B residue   92 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0870
   chunk 40 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 295 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.127970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.098684 restraints weight = 6929.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 2.83
r_work: 0.2999 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5592  Z= 0.202
  Angle     :  0.643   9.771   7615  Z= 0.339
  Chirality :  0.042   0.180    896
  Planarity :  0.006   0.079    923
  Dihedral  :  7.070  54.960    834
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.02 %
    Favored  : 84.38 %
  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: -2.11 (0.31), residues: 694
  helix: -0.12 (0.27), residues: 381
  sheet: -2.13 (0.75), residues: 49
  loop : -3.22 (0.30), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  68 
 HIS   0.006   0.001   HIS A  20 
 PHE   0.012   0.001   PHE A 534 
 TYR   0.021   0.001   TYR A 290 
 ARG   0.005   0.001   ARG A  24 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.556 
Fit side-chains
REVERT: A  211 MET cc_start: 0.6732 (tmm) cc_final: 0.6255 (ttp)
REVERT: A  253 GLU cc_start: 0.8266 (tp30) cc_final: 0.8063 (tp30)
REVERT: A  254 LYS cc_start: 0.8830 (pttm) cc_final: 0.8496 (pttm)
REVERT: A  382 MET cc_start: 0.5825 (mmm) cc_final: 0.5527 (mmt)
  outliers start: 15
  outliers final: 7
  residues processed: 96
  average time/residue: 0.1728
  time to fit residues: 21.8127
Evaluate side-chains
  85 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 59 optimal weight:    0.0170
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    0.2980
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.126496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.096942 restraints weight = 6964.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 2.84
r_work: 0.2972 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2986
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5592  Z= 0.160
  Angle     :  0.547   7.066   7615  Z= 0.288
  Chirality :  0.040   0.152    896
  Planarity :  0.005   0.053    923
  Dihedral  :  5.916  43.245    829
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.15 %
    Favored  : 81.77 %
  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 (0.32), residues: 694
  helix:  0.86 (0.29), residues: 373
  sheet: -1.54 (0.78), residues: 50
  loop : -3.06 (0.30), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  68 
 HIS   0.007   0.001   HIS A  20 
 PHE   0.012   0.001   PHE A 534 
 TYR   0.009   0.001   TYR A 290 
 ARG   0.006   0.000   ARG A  24 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A  211 MET cc_start: 0.6801 (tmm) cc_final: 0.6486 (ttp)
REVERT: A  253 GLU cc_start: 0.8158 (tp30) cc_final: 0.7804 (tp30)
REVERT: A  254 LYS cc_start: 0.8865 (pttm) cc_final: 0.8580 (pttm)
  outliers start: 12
  outliers final: 8
  residues processed: 85
  average time/residue: 0.1900
  time to fit residues: 20.7400
Evaluate side-chains
  78 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0060
   overall best weight:    0.7196

-------------------------------------------------------------------------------
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 = 0.3435 r_free = 0.3435 target = 0.123911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.094393 restraints weight = 7163.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.86
r_work: 0.2931 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.5031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5592  Z= 0.191
  Angle     :  0.553   7.213   7615  Z= 0.293
  Chirality :  0.041   0.139    896
  Planarity :  0.005   0.051    923
  Dihedral  :  5.803  50.246    827
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.97 %
    Favored  : 81.42 %
  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: -0.70 (0.33), residues: 694
  helix:  1.11 (0.29), residues: 390
  sheet: -1.26 (0.81), residues: 49
  loop : -2.94 (0.31), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  68 
 HIS   0.007   0.001   HIS A  20 
 PHE   0.016   0.001   PHE A 534 
 TYR   0.010   0.001   TYR A 526 
 ARG   0.008   0.001   ARG A  24 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A  211 MET cc_start: 0.6884 (tmm) cc_final: 0.6664 (ttp)
REVERT: A  253 GLU cc_start: 0.8027 (tp30) cc_final: 0.7725 (tp30)
  outliers start: 15
  outliers final: 9
  residues processed: 79
  average time/residue: 0.1850
  time to fit residues: 19.0537
Evaluate side-chains
  72 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0670
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.6920

-------------------------------------------------------------------------------
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 = 0.3438 r_free = 0.3438 target = 0.124110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.094804 restraints weight = 6954.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.82
r_work: 0.2940 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.5307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5592  Z= 0.174
  Angle     :  0.535   7.142   7615  Z= 0.282
  Chirality :  0.040   0.139    896
  Planarity :  0.005   0.047    923
  Dihedral  :  5.629  56.284    826
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.06 %
    Favored  : 79.51 %
  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: -0.43 (0.33), residues: 694
  helix:  1.29 (0.28), residues: 394
  sheet: -0.95 (0.82), residues: 50
  loop : -2.86 (0.32), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  68 
 HIS   0.007   0.001   HIS A  20 
 PHE   0.013   0.001   PHE A 534 
 TYR   0.011   0.001   TYR B  61 
 ARG   0.008   0.000   ARG A  24 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.549 
Fit side-chains
REVERT: A  253 GLU cc_start: 0.7914 (tp30) cc_final: 0.7586 (tp30)
  outliers start: 14
  outliers final: 9
  residues processed: 73
  average time/residue: 0.1907
  time to fit residues: 17.9960
Evaluate side-chains
  67 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0010
   chunk 44 optimal weight:    0.0670
   chunk 64 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0050
   chunk 50 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.3538

-------------------------------------------------------------------------------
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 = 0.3475 r_free = 0.3475 target = 0.127363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.097942 restraints weight = 6923.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.82
r_work: 0.2997 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.5403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5592  Z= 0.135
  Angle     :  0.517   7.012   7615  Z= 0.270
  Chirality :  0.039   0.139    896
  Planarity :  0.004   0.043    923
  Dihedral  :  5.421  58.029    826
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 18.92 %
    Favored  : 79.34 %
  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: -0.15 (0.34), residues: 694
  helix:  1.60 (0.29), residues: 390
  sheet: -0.87 (0.82), residues: 50
  loop : -2.82 (0.32), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  68 
 HIS   0.007   0.001   HIS A  20 
 PHE   0.009   0.001   PHE A 534 
 TYR   0.009   0.001   TYR B  61 
 ARG   0.006   0.000   ARG A  24 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A  253 GLU cc_start: 0.7743 (tp30) cc_final: 0.7392 (tp30)
  outliers start: 10
  outliers final: 7
  residues processed: 71
  average time/residue: 0.2136
  time to fit residues: 19.4505
Evaluate side-chains
  66 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 3 optimal weight:    0.2980
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.124676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.095119 restraints weight = 7040.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.83
r_work: 0.2954 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2943
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.5518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5592  Z= 0.175
  Angle     :  0.536   7.122   7615  Z= 0.281
  Chirality :  0.040   0.138    896
  Planarity :  0.004   0.044    923
  Dihedral  :  4.508  33.830    826
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.79 %
    Favored  : 78.30 %
  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: -0.06 (0.34), residues: 694
  helix:  1.50 (0.28), residues: 399
  sheet: -0.83 (0.83), residues: 50
  loop : -2.60 (0.34), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  68 
 HIS   0.007   0.001   HIS A  20 
 PHE   0.014   0.001   PHE A 534 
 TYR   0.008   0.001   TYR B  61 
 ARG   0.006   0.000   ARG A  24 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A  253 GLU cc_start: 0.7721 (tp30) cc_final: 0.7319 (tp30)
  outliers start: 11
  outliers final: 10
  residues processed: 70
  average time/residue: 0.2210
  time to fit residues: 19.8204
Evaluate side-chains
  69 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  663 PHE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0020
   chunk 58 optimal weight:    0.0040
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.4400

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.126955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.097566 restraints weight = 6888.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.81
r_work: 0.2983 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.5651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5592  Z= 0.145
  Angle     :  0.516   6.994   7615  Z= 0.269
  Chirality :  0.039   0.138    896
  Planarity :  0.004   0.042    923
  Dihedral  :  4.272  27.652    826
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.79 %
    Favored  : 77.95 %
  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:  0.10 (0.34), residues: 694
  helix:  1.76 (0.29), residues: 389
  sheet: -0.81 (0.83), residues: 50
  loop : -2.59 (0.33), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  68 
 HIS   0.007   0.001   HIS A  20 
 PHE   0.010   0.001   PHE A 534 
 TYR   0.008   0.001   TYR B  61 
 ARG   0.006   0.000   ARG A  24 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A  253 GLU cc_start: 0.7584 (tp30) cc_final: 0.7162 (tp30)
  outliers start: 13
  outliers final: 10
  residues processed: 74
  average time/residue: 0.1971
  time to fit residues: 18.7701
Evaluate side-chains
  67 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  663 PHE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0050
   chunk 23 optimal weight:    0.0030
   chunk 21 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0270
   chunk 50 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.2662

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.130099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.100837 restraints weight = 6878.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.82
r_work: 0.3015 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.5787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5592  Z= 0.129
  Angle     :  0.501   6.908   7615  Z= 0.261
  Chirality :  0.039   0.138    896
  Planarity :  0.004   0.041    923
  Dihedral  :  4.061  26.811    826
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 20.49 %
    Favored  : 77.60 %
  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:  0.25 (0.34), residues: 694
  helix:  1.98 (0.29), residues: 389
  sheet: -0.78 (0.84), residues: 50
  loop : -2.70 (0.32), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  68 
 HIS   0.007   0.001   HIS A  20 
 PHE   0.007   0.001   PHE A 534 
 TYR   0.009   0.001   TYR B  61 
 ARG   0.006   0.000   ARG A  24 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.610 
Fit side-chains
REVERT: A   96 LEU cc_start: 0.8635 (tp) cc_final: 0.8414 (tt)
REVERT: A  253 GLU cc_start: 0.7666 (tp30) cc_final: 0.7254 (tp30)
  outliers start: 11
  outliers final: 10
  residues processed: 72
  average time/residue: 0.2016
  time to fit residues: 18.6192
Evaluate side-chains
  70 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  663 PHE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9980
   chunk 1 optimal weight:    0.3980
   chunk 55 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0010
   chunk 53 optimal weight:    7.9990
   overall best weight:    0.4184

-------------------------------------------------------------------------------
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 = 0.3493 r_free = 0.3493 target = 0.129042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.099431 restraints weight = 6901.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.84
r_work: 0.3023 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.5824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5592  Z= 0.142
  Angle     :  0.511   6.977   7615  Z= 0.266
  Chirality :  0.039   0.138    896
  Planarity :  0.004   0.041    923
  Dihedral  :  4.042  26.369    826
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 20.14 %
    Favored  : 77.95 %
  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:  0.30 (0.34), residues: 694
  helix:  1.99 (0.29), residues: 386
  sheet: -0.71 (0.85), residues: 50
  loop : -2.59 (0.32), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  68 
 HIS   0.007   0.001   HIS A  20 
 PHE   0.010   0.001   PHE A 534 
 TYR   0.008   0.001   TYR B  61 
 ARG   0.007   0.000   ARG A  24 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A  253 GLU cc_start: 0.7592 (tp30) cc_final: 0.7167 (tp30)
  outliers start: 11
  outliers final: 11
  residues processed: 70
  average time/residue: 0.2090
  time to fit residues: 18.7248
Evaluate side-chains
  70 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  663 PHE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.126201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.096434 restraints weight = 7014.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.86
r_work: 0.2961 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.5854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5592  Z= 0.162
  Angle     :  0.522   7.046   7615  Z= 0.273
  Chirality :  0.040   0.137    896
  Planarity :  0.004   0.042    923
  Dihedral  :  4.113  26.000    826
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 20.14 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.34), residues: 694
  helix:  2.00 (0.28), residues: 384
  sheet: -0.66 (0.86), residues: 50
  loop : -2.53 (0.32), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  68 
 HIS   0.007   0.001   HIS A  20 
 PHE   0.012   0.001   PHE A 534 
 TYR   0.008   0.001   TYR B  61 
 ARG   0.007   0.000   ARG A  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3016.92 seconds
wall clock time: 52 minutes 25.95 seconds (3145.95 seconds total)