Starting phenix.real_space_refine
on Wed Mar 12 06:39:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cbb_45421/03_2025/9cbb_45421_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cbb_45421/03_2025/9cbb_45421.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cbb_45421/03_2025/9cbb_45421.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cbb_45421/03_2025/9cbb_45421.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cbb_45421/03_2025/9cbb_45421_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cbb_45421/03_2025/9cbb_45421_trim.cif"
  }
  resolution = 4.15
  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=  -0.000 sd=   0.039
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
     S      15      5.16       5
     C    2392      2.51       5
     N     587      2.21       5
     O     629      1.98       5
     H    3733      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7356
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 7344
          Classifications: {'peptide': 470}
          Link IDs: {'PTRANS': 25, 'TRANS': 444}
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'URC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.26, per 1000 atoms: 0.58
  Number of scatterers: 7356
  At special positions: 0
  Unit cell: (85.9845, 65.512, 70.4254, 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      15     16.00
     O     629      8.00
     N     587      7.00
     C    2392      6.00
     H    3733      1.00
    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: 1.89
  Conformation dependent library (CDL) restraints added in 650.2 milliseconds
  

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  854

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      84.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.993A  pdb=" N   VAL A  58 " --> pdb=" O   CYS A  54 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A  59 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 77
      removed outlier: 3.669A  pdb=" N   SER A  68 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TYR A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A  75 " --> pdb=" O   TYR A  71 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER A  76 " --> pdb=" O   GLY A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 92
      removed outlier: 3.619A  pdb=" N   LYS A  86 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 127
      removed outlier: 3.633A  pdb=" N   LEU A 108 " --> pdb=" O   ASP A 104 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   PHE A 117 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ALA A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 132
    Processing helix  chain 'A' and resid 136 through 157
      removed outlier: 3.683A  pdb=" N   ASN A 144 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ASN A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLY A 146 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 177
      removed outlier: 3.573A  pdb=" N   ILE A 168 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASP A 177 " --> pdb=" O   ILE A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 189
      Proline residue:  A 186  - end of helix
    Processing helix  chain 'A' and resid 197 through 220
      removed outlier: 3.964A  pdb=" N   LEU A 201 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY A 202 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE A 208 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS A 210 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLY A 216 " --> pdb=" O   GLY A 212 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLN A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 237
      removed outlier: 3.521A  pdb=" N   LEU A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 252
      removed outlier: 3.584A  pdb=" N   ALA A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      Proline residue:  A 250  - end of helix
    Processing helix  chain 'A' and resid 255 through 262
      removed outlier: 3.522A  pdb=" N   LEU A 259 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU A 260 " --> pdb=" O   PRO A 256 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU A 261 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 4.135A  pdb=" N   LYS A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 299
      removed outlier: 3.816A  pdb=" N   VAL A 289 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LEU A 290 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLU A 292 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER A 293 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 309
      removed outlier: 4.077A  pdb=" N   LEU A 308 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 304 through 309'
    Processing helix  chain 'A' and resid 310 through 312
      No H-bonds generated for 'chain 'A' and resid 310 through 312'
    Processing helix  chain 'A' and resid 313 through 329
      removed outlier: 4.228A  pdb=" N   VAL A 318 " --> pdb=" O   ARG A 314 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   THR A 319 " --> pdb=" O   TRP A 315 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A 322 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET A 324 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   TYR A 327 " --> pdb=" O   THR A 323 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLN A 328 " --> pdb=" O   MET A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 338
    Processing helix  chain 'A' and resid 338 through 346
      removed outlier: 3.541A  pdb=" N   ALA A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 371
      removed outlier: 4.064A  pdb=" N   LEU A 358 " --> pdb=" O   PRO A 354 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   SER A 359 " --> pdb=" O   TYR A 355 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   THR A 360 " --> pdb=" O   VAL A 356 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLY A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLU A 364 " --> pdb=" O   THR A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 379
      removed outlier: 4.483A  pdb=" N   GLU A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   HIS A 377 " --> pdb=" O   LEU A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 405
      removed outlier: 3.684A  pdb=" N   LEU A 384 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 388 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLY A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 393 " --> pdb=" O   GLY A 389 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 429
      removed outlier: 3.718A  pdb=" N   VAL A 417 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER A 428 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 442
      removed outlier: 3.884A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU A 440 " --> pdb=" O   ILE A 436 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE A 442 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 477
      removed outlier: 3.787A  pdb=" N   PHE A 451 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ILE A 452 " --> pdb=" O   PRO A 448 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR A 456 " --> pdb=" O   ILE A 452 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL A 457 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      Proline residue:  A 470  - end of helix
    Processing helix  chain 'A' and resid 480 through 499
      removed outlier: 4.162A  pdb=" N   PHE A 484 " --> pdb=" O   CYS A 480 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   PHE A 497 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 498 " --> pdb=" O   TYR A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 519
      removed outlier: 3.650A  pdb=" N   ILE A 510 " --> pdb=" O   THR A 506 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG A 517 " --> pdb=" O   ALA A 513 " (cutoff:3.500A)

    208 hydrogen bonds defined for protein.
    624 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.43

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 3725
        1.03 -     1.22: 11
        1.22 -     1.42: 1525
        1.42 -     1.62: 2165
        1.62 -     1.81: 22
  Bond restraints: 7448
  Sorted by residual:
  bond pdb=" C4  URC A 601 "
       pdb=" N3  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.352  1.476 -0.124 2.00e-02 2.50e+03 3.82e+01
  bond pdb=" C4  URC A 601 "
       pdb=" N9  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.352  1.471 -0.119 2.00e-02 2.50e+03 3.52e+01
  bond pdb=" C2  URC A 601 "
       pdb=" N1  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.375  1.487 -0.112 2.00e-02 2.50e+03 3.15e+01
  bond pdb=" C4  URC A 601 "
       pdb=" C5  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.358  1.467 -0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" C2  URC A 601 "
       pdb=" N3  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.376  1.484 -0.108 2.00e-02 2.50e+03 2.94e+01
  ... (remaining 7443 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 12918
        1.85 -     3.70: 509
        3.70 -     5.55: 68
        5.55 -     7.40: 12
        7.40 -     9.25: 5
  Bond angle restraints: 13512
  Sorted by residual:
  angle pdb=" N   ILE A 335 "
        pdb=" CA  ILE A 335 "
        pdb=" C   ILE A 335 "
      ideal   model   delta    sigma   weight residual
     110.30  105.40    4.90 9.70e-01 1.06e+00 2.55e+01
  angle pdb=" C   ILE A 335 "
        pdb=" CA  ILE A 335 "
        pdb=" CB  ILE A 335 "
      ideal   model   delta    sigma   weight residual
     111.81  117.36   -5.55 1.25e+00 6.40e-01 1.97e+01
  angle pdb=" C   ILE A 353 "
        pdb=" CA  ILE A 353 "
        pdb=" CB  ILE A 353 "
      ideal   model   delta    sigma   weight residual
     111.36  117.85   -6.49 1.82e+00 3.02e-01 1.27e+01
  angle pdb=" CB  ARG A 381 "
        pdb=" CG  ARG A 381 "
        pdb=" CD  ARG A 381 "
      ideal   model   delta    sigma   weight residual
     111.30  118.88   -7.58 2.30e+00 1.89e-01 1.09e+01
  angle pdb=" CA  ARG A 381 "
        pdb=" CB  ARG A 381 "
        pdb=" CG  ARG A 381 "
      ideal   model   delta    sigma   weight residual
     114.10  120.45   -6.35 2.00e+00 2.50e-01 1.01e+01
  ... (remaining 13507 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.66: 3065
       16.66 -    33.33: 303
       33.33 -    49.99: 85
       49.99 -    66.65: 41
       66.65 -    83.32: 6
  Dihedral angle restraints: 3500
    sinusoidal: 1880
      harmonic: 1620
  Sorted by residual:
  dihedral pdb=" CA  LEU A 185 "
           pdb=" C   LEU A 185 "
           pdb=" N   PRO A 186 "
           pdb=" CA  PRO A 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.49  -24.51     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" CA  HIS A  97 "
           pdb=" C   HIS A  97 "
           pdb=" N   GLY A  98 "
           pdb=" CA  GLY A  98 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.87  -22.13     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  ASN A 518 "
           pdb=" C   ASN A 518 "
           pdb=" N   LYS A 519 "
           pdb=" CA  LYS A 519 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.34  -20.66     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 3497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 360
       0.033 -    0.066: 160
       0.066 -    0.099: 52
       0.099 -    0.132: 18
       0.132 -    0.164: 5
  Chirality restraints: 595
  Sorted by residual:
  chirality pdb=" CA  PRO A 256 "
            pdb=" N   PRO A 256 "
            pdb=" C   PRO A 256 "
            pdb=" CB  PRO A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.16 2.00e-01 2.50e+01 6.76e-01
  chirality pdb=" CA  PRO A 186 "
            pdb=" N   PRO A 186 "
            pdb=" C   PRO A 186 "
            pdb=" CB  PRO A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.13e-01
  chirality pdb=" CA  ASN A 504 "
            pdb=" N   ASN A 504 "
            pdb=" C   ASN A 504 "
            pdb=" CB  ASN A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.59e-01
  ... (remaining 592 not shown)

  Planarity restraints: 1070
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 335 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.84e+00
        pdb=" N   TRP A 336 "   -0.038 2.00e-02 2.50e+03
        pdb=" CA  TRP A 336 "    0.009 2.00e-02 2.50e+03
        pdb=" H   TRP A 336 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 184 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.03e+00
        pdb=" C   VAL A 184 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL A 184 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 185 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 380 "   -0.149 9.50e-02 1.11e+02   5.00e-02 3.01e+00
        pdb=" NE  ARG A 380 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 380 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 380 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 380 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG A 380 "    0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG A 380 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 380 "   -0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A 380 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1067 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 756
        2.24 -     2.83: 16254
        2.83 -     3.42: 19470
        3.42 -     4.01: 24751
        4.01 -     4.60: 38273
  Nonbonded interactions: 99504
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 197 "
            pdb=" HG  SER A 200 "
     model   vdw
     1.646 2.450
  nonbonded pdb=" O   THR A 319 "
            pdb=" HG1 THR A 323 "
     model   vdw
     1.709 2.450
  nonbonded pdb=" O   SER A 190 "
            pdb="HH22 ARG A 257 "
     model   vdw
     1.714 2.450
  nonbonded pdb=" O   LEU A 109 "
            pdb=" HG1 THR A 113 "
     model   vdw
     1.714 2.450
  nonbonded pdb=" O   LEU A 398 "
            pdb=" HG1 THR A 401 "
     model   vdw
     1.722 2.450
  ... (remaining 99499 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  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:             0.130
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.770
  Find NCS groups from input model:        0.050
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
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      :  0.007   0.124   3715  Z= 0.445
  Angle     :  0.921   9.252   5063  Z= 0.461
  Chirality :  0.044   0.164    595
  Planarity :  0.007   0.066    626
  Dihedral  : 14.258  83.316   1303
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.08 (0.36), residues: 468
  helix: -1.06 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.79 (0.50), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 315 
 HIS   0.001   0.000   HIS A  97 
 PHE   0.014   0.002   PHE A 514 
 TYR   0.015   0.001   TYR A 188 
 ARG   0.010   0.001   ARG A 137 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.702 
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: symmetry clash
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8820 (t0) cc_final: 0.8594 (t0)
REVERT: A   95 ARG cc_start: 0.7787 (tpp-160) cc_final: 0.7336 (ttt180)
REVERT: A  155 MET cc_start: 0.7761 (mmt) cc_final: 0.7477 (mmm)
REVERT: A  166 MET cc_start: 0.8848 (pmm) cc_final: 0.8562 (pmm)
REVERT: A  271 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8748 (mmtp)
REVERT: A  297 ARG cc_start: 0.7946 (ptt180) cc_final: 0.6917 (tpm170)
REVERT: A  359 SER cc_start: 0.8383 (m) cc_final: 0.7812 (t)
REVERT: A  420 LEU cc_start: 0.8973 (mp) cc_final: 0.8652 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2965
  time to fit residues: 41.5732
Evaluate side-chains
  102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.161056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.133388 restraints weight = 21334.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.138881 restraints weight = 10355.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.142543 restraints weight = 6334.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3715  Z= 0.217
  Angle     :  0.655   7.261   5063  Z= 0.356
  Chirality :  0.039   0.130    595
  Planarity :  0.005   0.035    626
  Dihedral  :  5.012  22.746    504
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  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: -1.38 (0.37), residues: 468
  helix: -0.39 (0.27), residues: 335
  sheet:  None (None), residues: 0
  loop : -2.05 (0.52), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 459 
 HIS   0.004   0.001   HIS A 139 
 PHE   0.016   0.002   PHE A 214 
 TYR   0.010   0.001   TYR A 188 
 ARG   0.003   0.000   ARG A 171 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.602 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.7266 (ttt180)
REVERT: A  271 LYS cc_start: 0.9124 (mmmt) cc_final: 0.8823 (mmtp)
REVERT: A  297 ARG cc_start: 0.8076 (ptt180) cc_final: 0.7136 (tpm170)
REVERT: A  359 SER cc_start: 0.8537 (m) cc_final: 0.8039 (t)
REVERT: A  420 LEU cc_start: 0.9050 (mp) cc_final: 0.8817 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2874
  time to fit residues: 41.1218
Evaluate side-chains
  102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    0.4980
   chunk 24 optimal weight:    5.9990
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0370
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.160513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.131279 restraints weight = 21713.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.136941 restraints weight = 10701.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.140738 restraints weight = 6552.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3715  Z= 0.172
  Angle     :  0.584   6.895   5063  Z= 0.307
  Chirality :  0.038   0.135    595
  Planarity :  0.005   0.036    626
  Dihedral  :  4.784  20.396    504
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  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: -0.96 (0.39), residues: 468
  helix: -0.07 (0.28), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.89 (0.54), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 459 
 HIS   0.008   0.002   HIS A 407 
 PHE   0.012   0.001   PHE A 214 
 TYR   0.007   0.001   TYR A 188 
 ARG   0.003   0.000   ARG A 171 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.583 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.7741 (tpp-160) cc_final: 0.7385 (ttt180)
REVERT: A  271 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8795 (mmtp)
REVERT: A  297 ARG cc_start: 0.8142 (ptt180) cc_final: 0.7169 (tpm170)
REVERT: A  337 PHE cc_start: 0.8014 (m-10) cc_final: 0.7801 (m-10)
REVERT: A  359 SER cc_start: 0.8549 (m) cc_final: 0.8158 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.2853
  time to fit residues: 40.5984
Evaluate side-chains
  100 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.159569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.130642 restraints weight = 22356.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.135991 restraints weight = 10603.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.139502 restraints weight = 6506.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3715  Z= 0.257
  Angle     :  0.609   7.237   5063  Z= 0.330
  Chirality :  0.038   0.133    595
  Planarity :  0.005   0.030    626
  Dihedral  :  4.683  22.064    504
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  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: -0.88 (0.39), residues: 468
  helix:  0.02 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -2.01 (0.55), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 336 
 HIS   0.003   0.001   HIS A 139 
 PHE   0.009   0.001   PHE A 235 
 TYR   0.021   0.001   TYR A 188 
 ARG   0.005   0.001   ARG A 137 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.825 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.7916 (tpp-160) cc_final: 0.7387 (ttt180)
REVERT: A  271 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8816 (mmtp)
REVERT: A  297 ARG cc_start: 0.8313 (ptt180) cc_final: 0.7355 (tpm170)
REVERT: A  359 SER cc_start: 0.8741 (m) cc_final: 0.8339 (t)
REVERT: A  420 LEU cc_start: 0.9124 (mp) cc_final: 0.8855 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.3392
  time to fit residues: 48.6925
Evaluate side-chains
  99 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0570
   chunk 33 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 473 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.159129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.130152 restraints weight = 21849.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135730 restraints weight = 10569.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.139408 restraints weight = 6446.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3715  Z= 0.173
  Angle     :  0.556   6.940   5063  Z= 0.293
  Chirality :  0.038   0.134    595
  Planarity :  0.004   0.030    626
  Dihedral  :  4.641  22.202    504
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  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: -0.58 (0.40), residues: 468
  helix:  0.23 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.85 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 336 
 HIS   0.002   0.000   HIS A 139 
 PHE   0.012   0.001   PHE A 235 
 TYR   0.018   0.001   TYR A 188 
 ARG   0.003   0.000   ARG A 137 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.582 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7347 (ttt180)
REVERT: A  155 MET cc_start: 0.7901 (mmt) cc_final: 0.7544 (mmp)
REVERT: A  271 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8801 (mmtp)
REVERT: A  297 ARG cc_start: 0.8249 (ptt180) cc_final: 0.7289 (tpm170)
REVERT: A  359 SER cc_start: 0.8398 (m) cc_final: 0.7999 (t)
REVERT: A  420 LEU cc_start: 0.9120 (mp) cc_final: 0.8901 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2996
  time to fit residues: 41.9506
Evaluate side-chains
  102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.157973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.129448 restraints weight = 22160.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.134908 restraints weight = 10490.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.138326 restraints weight = 6401.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3715  Z= 0.226
  Angle     :  0.586   7.541   5063  Z= 0.313
  Chirality :  0.038   0.131    595
  Planarity :  0.005   0.036    626
  Dihedral  :  4.554  21.764    504
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  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: -0.52 (0.40), residues: 468
  helix:  0.20 (0.29), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.58 (0.59), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 336 
 HIS   0.002   0.001   HIS A 139 
 PHE   0.007   0.001   PHE A  88 
 TYR   0.011   0.001   TYR A 188 
 ARG   0.007   0.000   ARG A 171 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.513 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7336 (ttt180)
REVERT: A  155 MET cc_start: 0.8034 (mmt) cc_final: 0.7071 (mmm)
REVERT: A  271 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8824 (mmtp)
REVERT: A  297 ARG cc_start: 0.8260 (ptt180) cc_final: 0.7300 (tpm170)
REVERT: A  359 SER cc_start: 0.8520 (m) cc_final: 0.8146 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2494
  time to fit residues: 36.2970
Evaluate side-chains
  100 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.158913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.129747 restraints weight = 22322.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.135259 restraints weight = 10532.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.138819 restraints weight = 6433.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3715  Z= 0.181
  Angle     :  0.562   7.041   5063  Z= 0.295
  Chirality :  0.038   0.132    595
  Planarity :  0.004   0.034    626
  Dihedral  :  4.524  22.026    504
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    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: -0.32 (0.40), residues: 468
  helix:  0.34 (0.29), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.53 (0.60), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  93 
 HIS   0.003   0.001   HIS A 377 
 PHE   0.011   0.001   PHE A 235 
 TYR   0.009   0.001   TYR A 188 
 ARG   0.005   0.000   ARG A 171 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.584 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.7889 (tpp-160) cc_final: 0.7313 (ttt180)
REVERT: A  109 LEU cc_start: 0.8598 (mt) cc_final: 0.8339 (mt)
REVERT: A  271 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8816 (mmtp)
REVERT: A  297 ARG cc_start: 0.8256 (ptt180) cc_final: 0.7301 (tpm170)
REVERT: A  359 SER cc_start: 0.8386 (m) cc_final: 0.8034 (t)
REVERT: A  391 MET cc_start: 0.8223 (ppp) cc_final: 0.7943 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2723
  time to fit residues: 39.4540
Evaluate side-chains
  102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0570
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.158944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.130132 restraints weight = 22367.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135643 restraints weight = 10430.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.138702 restraints weight = 6323.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3715  Z= 0.186
  Angle     :  0.562   7.222   5063  Z= 0.295
  Chirality :  0.038   0.131    595
  Planarity :  0.004   0.035    626
  Dihedral  :  4.463  21.582    504
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  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: -0.27 (0.40), residues: 468
  helix:  0.39 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.52 (0.60), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 336 
 HIS   0.003   0.001   HIS A 377 
 PHE   0.008   0.001   PHE A 514 
 TYR   0.009   0.001   TYR A 188 
 ARG   0.006   0.000   ARG A 171 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.575 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7278 (ttt180)
REVERT: A  155 MET cc_start: 0.8089 (mmt) cc_final: 0.6959 (mmt)
REVERT: A  271 LYS cc_start: 0.9134 (mmmt) cc_final: 0.8824 (mmtp)
REVERT: A  297 ARG cc_start: 0.8279 (ptt180) cc_final: 0.7310 (tpm170)
REVERT: A  359 SER cc_start: 0.8423 (m) cc_final: 0.8046 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2703
  time to fit residues: 39.1627
Evaluate side-chains
  102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 14 optimal weight:    0.1980
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 27 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.157761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.128705 restraints weight = 22239.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.134135 restraints weight = 10592.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.137374 restraints weight = 6528.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3715  Z= 0.169
  Angle     :  0.571   7.118   5063  Z= 0.293
  Chirality :  0.038   0.129    595
  Planarity :  0.004   0.042    626
  Dihedral  :  4.456  21.944    504
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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 (0.40), residues: 468
  helix:  0.36 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.51 (0.60), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  93 
 HIS   0.002   0.001   HIS A 377 
 PHE   0.007   0.001   PHE A 441 
 TYR   0.008   0.001   TYR A 188 
 ARG   0.005   0.000   ARG A 171 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.620 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 ASN cc_start: 0.8649 (t0) cc_final: 0.8427 (t0)
REVERT: A   95 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.7263 (ttt180)
REVERT: A  155 MET cc_start: 0.8016 (mmt) cc_final: 0.6829 (mmt)
REVERT: A  166 MET cc_start: 0.8984 (pmm) cc_final: 0.8538 (pmm)
REVERT: A  271 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8803 (mmtp)
REVERT: A  296 GLN cc_start: 0.8093 (mm110) cc_final: 0.7535 (mm110)
REVERT: A  297 ARG cc_start: 0.8255 (ptt180) cc_final: 0.7287 (tpm170)
REVERT: A  359 SER cc_start: 0.8208 (m) cc_final: 0.7826 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2805
  time to fit residues: 39.9098
Evaluate side-chains
  103 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0570
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.158948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.130256 restraints weight = 22761.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.135835 restraints weight = 10527.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.139441 restraints weight = 6339.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3715  Z= 0.188
  Angle     :  0.566   7.099   5063  Z= 0.297
  Chirality :  0.038   0.130    595
  Planarity :  0.004   0.039    626
  Dihedral  :  4.411  22.033    504
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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: -0.26 (0.40), residues: 468
  helix:  0.41 (0.29), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.57 (0.60), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 336 
 HIS   0.002   0.001   HIS A 377 
 PHE   0.012   0.001   PHE A 514 
 TYR   0.007   0.001   TYR A 188 
 ARG   0.005   0.000   ARG A 171 

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.515 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7244 (ttt180)
REVERT: A  155 MET cc_start: 0.8077 (mmt) cc_final: 0.6876 (mmt)
REVERT: A  271 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8788 (mmtp)
REVERT: A  296 GLN cc_start: 0.8070 (mm110) cc_final: 0.7518 (mm110)
REVERT: A  297 ARG cc_start: 0.8277 (ptt180) cc_final: 0.7283 (tpm170)
REVERT: A  359 SER cc_start: 0.8268 (m) cc_final: 0.7838 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2649
  time to fit residues: 38.2709
Evaluate side-chains
  101 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 29 optimal weight:    0.0020
   chunk 7 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 41 optimal weight:    0.3980
   overall best weight:    0.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.159120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.131364 restraints weight = 22198.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.137046 restraints weight = 10215.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.140702 restraints weight = 6026.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3715  Z= 0.162
  Angle     :  0.558   7.036   5063  Z= 0.284
  Chirality :  0.038   0.132    595
  Planarity :  0.004   0.039    626
  Dihedral  :  4.388  21.365    504
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    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: -0.09 (0.41), residues: 468
  helix:  0.50 (0.29), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.48 (0.62), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 459 
 HIS   0.002   0.000   HIS A 377 
 PHE   0.006   0.001   PHE A 441 
 TYR   0.009   0.001   TYR A  71 
 ARG   0.005   0.000   ARG A 171 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3340.68 seconds
wall clock time: 57 minutes 37.23 seconds (3457.23 seconds total)