Starting phenix.real_space_refine
on Wed Sep 17 14:51:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yf0_39206/09_2025/8yf0_39206.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yf0_39206/09_2025/8yf0_39206.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yf0_39206/09_2025/8yf0_39206.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yf0_39206/09_2025/8yf0_39206.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yf0_39206/09_2025/8yf0_39206.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yf0_39206/09_2025/8yf0_39206.cif"
  }
  resolution = 3.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.043
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      70      5.16       5
     C    5989      2.51       5
     N    1519      2.21       5
     O    1603      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9181
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 567, 4505
          Classifications: {'peptide': 567}
          Link IDs: {'PTRANS': 13, 'TRANS': 553}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 4676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4676
          Classifications: {'peptide': 592}
          Link IDs: {'PTRANS': 15, 'TRANS': 576}
          Chain breaks: 1
  Time building chain proxies: 1.85, per 1000 atoms: 0.20
  Number of scatterers: 9181
  At special positions: 0
  Unit cell: (117.432, 100.656, 129.548, 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      70     16.00
     O    1603      8.00
     N    1519      7.00
     C    5989      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 289.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 4 sheets defined
      73.6% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'B' and resid 133 through 160
      removed outlier: 4.287A  pdb=" N   GLY B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 188
      removed outlier: 3.932A  pdb=" N   LEU B 174 " --> pdb=" O   PHE B 170 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ALA B 175 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 194
      removed outlier: 3.892A  pdb=" N   GLU B 194 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 197
      No H-bonds generated for 'chain 'B' and resid 195 through 197'
    Processing helix  chain 'B' and resid 200 through 230
      removed outlier: 3.964A  pdb=" N   MET B 206 " --> pdb=" O   SER B 202 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   GLY B 208 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LEU B 209 " --> pdb=" O   GLY B 205 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   ASP B 227 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   ARG B 228 " --> pdb=" O   GLY B 224 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLY B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 250
      removed outlier: 3.621A  pdb=" N   ASN B 242 " --> pdb=" O   SER B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 270
      removed outlier: 3.958A  pdb=" N   LEU B 259 " --> pdb=" O   TYR B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 284
      removed outlier: 3.543A  pdb=" N   ILE B 275 " --> pdb=" O   GLY B 271 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   PHE B 283 " --> pdb=" O   TYR B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 295
      removed outlier: 3.578A  pdb=" N   HIS B 292 " --> pdb=" O   LYS B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 315
      removed outlier: 3.818A  pdb=" N   TRP B 300 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE B 315 " --> pdb=" O   ALA B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 322
      removed outlier: 3.628A  pdb=" N   SER B 321 " --> pdb=" O   TYR B 318 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   PHE B 322 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 318 through 322'
    Processing helix  chain 'B' and resid 332 through 352
      removed outlier: 3.580A  pdb=" N   LEU B 338 " --> pdb=" O   ARG B 334 " (cutoff:3.500A)
      Proline residue:  B 343  - end of helix
    Processing helix  chain 'B' and resid 357 through 365
      removed outlier: 3.908A  pdb=" N   PHE B 361 " --> pdb=" O   SER B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 385
      removed outlier: 3.783A  pdb=" N   THR B 380 " --> pdb=" O   GLN B 376 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ASN B 381 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 403
    Processing helix  chain 'B' and resid 416 through 439
      removed outlier: 3.566A  pdb=" N   GLY B 421 " --> pdb=" O   TYR B 417 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 467
      removed outlier: 4.126A  pdb=" N   PHE B 459 " --> pdb=" O   PHE B 455 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   SER B 460 " --> pdb=" O   THR B 456 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   TYR B 461 " --> pdb=" O   MET B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 482
      removed outlier: 4.169A  pdb=" N   MET B 471 " --> pdb=" O   TRP B 467 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   SER B 482 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 622
      removed outlier: 4.672A  pdb=" N   GLU B 592 " --> pdb=" O   THR B 588 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   GLY B 593 " --> pdb=" O   GLY B 589 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   MET B 596 " --> pdb=" O   GLU B 592 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LEU B 609 " --> pdb=" O   THR B 605 " (cutoff:3.500A)
      Proline residue:  B 610  - end of helix
      removed outlier: 3.868A  pdb=" N   VAL B 614 " --> pdb=" O   PRO B 610 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER B 615 " --> pdb=" O   GLY B 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 644
      removed outlier: 4.307A  pdb=" N   ALA B 629 " --> pdb=" O   LEU B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 649 through 677
    Processing helix  chain 'B' and resid 681 through 708
      removed outlier: 3.833A  pdb=" N   ILE B 701 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   SER B 706 " --> pdb=" O   SER B 702 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 160
    Processing helix  chain 'C' and resid 162 through 188
      removed outlier: 3.586A  pdb=" N   TRP C 166 " --> pdb=" O   GLY C 162 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA C 175 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 196
    Processing helix  chain 'C' and resid 200 through 205
      removed outlier: 4.297A  pdb=" N   GLY C 205 " --> pdb=" O   SER C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 230
      removed outlier: 4.181A  pdb=" N   VAL C 211 " --> pdb=" O   LEU C 207 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   TYR C 212 " --> pdb=" O   GLY C 208 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG C 228 " --> pdb=" O   GLY C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 252
      removed outlier: 3.694A  pdb=" N   SER C 250 " --> pdb=" O   ALA C 246 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   PHE C 251 " --> pdb=" O   PHE C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 271
      removed outlier: 4.010A  pdb=" N   GLY C 271 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 282
    Processing helix  chain 'C' and resid 288 through 295
    Processing helix  chain 'C' and resid 295 through 315
      removed outlier: 4.413A  pdb=" N   PHE C 299 " --> pdb=" O   TRP C 295 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY C 304 " --> pdb=" O   TRP C 300 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 331 through 340
    Processing helix  chain 'C' and resid 341 through 352
    Processing helix  chain 'C' and resid 357 through 365
      removed outlier: 3.644A  pdb=" N   PHE C 361 " --> pdb=" O   SER C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 366 through 385
      removed outlier: 3.528A  pdb=" N   ALA C 370 " --> pdb=" O   LYS C 366 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ARG C 383 " --> pdb=" O   ASP C 379 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ALA C 384 " --> pdb=" O   THR C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 400
      removed outlier: 4.723A  pdb=" N   VAL C 391 " --> pdb=" O   HIS C 387 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   PHE C 392 " --> pdb=" O   PRO C 388 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   SER C 393 " --> pdb=" O   GLU C 389 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   VAL C 394 " --> pdb=" O   ARG C 390 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 439
      removed outlier: 3.732A  pdb=" N   PHE C 439 " --> pdb=" O   PHE C 435 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 466
      removed outlier: 3.689A  pdb=" N   GLY C 452 " --> pdb=" O   LEU C 448 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   PHE C 459 " --> pdb=" O   PHE C 455 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   SER C 460 " --> pdb=" O   THR C 456 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLY C 463 " --> pdb=" O   PHE C 459 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 466 through 483
    Processing helix  chain 'C' and resid 590 through 622
      Proline residue:  C 610  - end of helix
      removed outlier: 4.030A  pdb=" N   ASP C 620 " --> pdb=" O   ALA C 616 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   LYS C 621 " --> pdb=" O   LEU C 617 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE C 622 " --> pdb=" O   LEU C 618 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 626 through 644
    Processing helix  chain 'C' and resid 647 through 677
      removed outlier: 4.041A  pdb=" N   VAL C 661 " --> pdb=" O   LEU C 657 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ASN C 667 " --> pdb=" O   ILE C 663 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ALA C 668 " --> pdb=" O   ALA C 664 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   LEU C 669 " --> pdb=" O   SER C 665 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ASP C 670 " --> pdb=" O   TRP C 666 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 678 through 707
      removed outlier: 4.638A  pdb=" N   THR C 683 " --> pdb=" O   SER C 679 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   THR C 684 " --> pdb=" O   ASP C 680 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 713 through 726
    Processing sheet with id=AA1, first strand: chain 'B' and resid 485 through 487
      removed outlier: 3.615A  pdb=" N   ILE B 505 " --> pdb=" O   LYS B 485 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 521 through 526
      removed outlier: 6.346A  pdb=" N   LYS B 522 " --> pdb=" O   ASN B 543 " (cutoff:3.500A)
      removed outlier: 8.593A  pdb=" N   PHE B 545 " --> pdb=" O   LYS B 522 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   VAL B 524 " --> pdb=" O   PHE B 545 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 504 through 507
      removed outlier: 5.965A  pdb=" N   GLN C 504 " --> pdb=" O   SER C 525 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   GLU C 527 " --> pdb=" O   GLN C 504 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   HIS C 506 " --> pdb=" O   GLU C 527 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 530 through 532
      removed outlier: 5.780A  pdb=" N   PHE C 531 " --> pdb=" O   ILE C 552 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    595 hydrogen bonds defined for protein.
    1779 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: 1.41

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2844
        1.34 -     1.46: 1917
        1.46 -     1.58: 4563
        1.58 -     1.70: 0
        1.70 -     1.81: 112
  Bond restraints: 9436
  Sorted by residual:
  bond pdb=" N   TYR B 152 "
       pdb=" CA  TYR B 152 "
    ideal  model  delta    sigma   weight residual
    1.459  1.425  0.034 1.17e-02 7.31e+03 8.26e+00
  bond pdb=" CA  TYR B 152 "
       pdb=" C   TYR B 152 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.026 1.24e-02 6.50e+03 4.54e+00
  bond pdb=" C   GLN B 151 "
       pdb=" N   TYR B 152 "
    ideal  model  delta    sigma   weight residual
    1.334  1.308  0.026 1.23e-02 6.61e+03 4.31e+00
  bond pdb=" CG1 ILE B 210 "
       pdb=" CD1 ILE B 210 "
    ideal  model  delta    sigma   weight residual
    1.513  1.448  0.065 3.90e-02 6.57e+02 2.75e+00
  bond pdb=" C   THR C 456 "
       pdb=" O   THR C 456 "
    ideal  model  delta    sigma   weight residual
    1.236  1.220  0.017 1.26e-02 6.30e+03 1.76e+00
  ... (remaining 9431 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 12519
        1.82 -     3.63: 191
        3.63 -     5.45: 46
        5.45 -     7.26: 6
        7.26 -     9.08: 2
  Bond angle restraints: 12764
  Sorted by residual:
  angle pdb=" N   TYR B 152 "
        pdb=" CA  TYR B 152 "
        pdb=" C   TYR B 152 "
      ideal   model   delta    sigma   weight residual
     110.97  107.08    3.89 1.09e+00 8.42e-01 1.27e+01
  angle pdb=" CB  MET B 634 "
        pdb=" CG  MET B 634 "
        pdb=" SD  MET B 634 "
      ideal   model   delta    sigma   weight residual
     112.70  121.78   -9.08 3.00e+00 1.11e-01 9.15e+00
  angle pdb=" C   SER C 272 "
        pdb=" N   ILE C 273 "
        pdb=" CA  ILE C 273 "
      ideal   model   delta    sigma   weight residual
     120.33  122.59   -2.26 8.00e-01 1.56e+00 8.00e+00
  angle pdb=" C   PHE B 640 "
        pdb=" N   PHE B 641 "
        pdb=" CA  PHE B 641 "
      ideal   model   delta    sigma   weight residual
     121.14  116.23    4.91 1.75e+00 3.27e-01 7.86e+00
  angle pdb=" C   ASP B 586 "
        pdb=" CA  ASP B 586 "
        pdb=" CB  ASP B 586 "
      ideal   model   delta    sigma   weight residual
     110.42  115.96   -5.54 1.99e+00 2.53e-01 7.74e+00
  ... (remaining 12759 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 4785
       17.78 -    35.56: 486
       35.56 -    53.35: 79
       53.35 -    71.13: 22
       71.13 -    88.91: 3
  Dihedral angle restraints: 5375
    sinusoidal: 2080
      harmonic: 3295
  Sorted by residual:
  dihedral pdb=" CA  HIS C 292 "
           pdb=" C   HIS C 292 "
           pdb=" N   LEU C 293 "
           pdb=" CA  LEU C 293 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.63   16.37     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  TRP C 222 "
           pdb=" C   TRP C 222 "
           pdb=" N   GLY C 223 "
           pdb=" CA  GLY C 223 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.65   16.35     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  VAL C 189 "
           pdb=" C   VAL C 189 "
           pdb=" N   LEU C 190 "
           pdb=" CA  LEU C 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.75   16.25     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 5372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 938
       0.036 -    0.072: 328
       0.072 -    0.107: 82
       0.107 -    0.143: 20
       0.143 -    0.179: 3
  Chirality restraints: 1371
  Sorted by residual:
  chirality pdb=" CG  LEU B 689 "
            pdb=" CB  LEU B 689 "
            pdb=" CD1 LEU B 689 "
            pdb=" CD2 LEU B 689 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.00e-01
  chirality pdb=" CG  LEU B 603 "
            pdb=" CB  LEU B 603 "
            pdb=" CD1 LEU B 603 "
            pdb=" CD2 LEU B 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.33e-01
  chirality pdb=" CB  THR C 456 "
            pdb=" CA  THR C 456 "
            pdb=" OG1 THR C 456 "
            pdb=" CG2 THR C 456 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.79e-01
  ... (remaining 1368 not shown)

  Planarity restraints: 1606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 468 "   -0.036 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO B 469 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B 469 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 469 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 222 "    0.012 2.00e-02 2.50e+03   1.10e-02 3.02e+00
        pdb=" CG  TRP C 222 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 222 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 222 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 222 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 222 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 222 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 222 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 222 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 222 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 220 "    0.014 2.00e-02 2.50e+03   1.22e-02 2.60e+00
        pdb=" CG  PHE B 220 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 220 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 220 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 220 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 220 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 220 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1603 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2307
        2.80 -     3.32: 9479
        3.32 -     3.85: 15436
        3.85 -     4.37: 17042
        4.37 -     4.90: 29059
  Nonbonded interactions: 73323
  Sorted by model distance:
  nonbonded pdb=" O   GLN B 253 "
            pdb=" OG1 THR B 257 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OH  TYR C 169 "
            pdb=" O   TRP C 295 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OH  TYR B 279 "
            pdb=" O   PRO B 355 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   TYR B 443 "
            pdb=" OG1 THR B 447 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OD2 ASP B 196 "
            pdb=" NE1 TRP B 333 "
     model   vdw
     2.295 3.120
  ... (remaining 73318 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = (chain 'C' and resid 133 through 709)
}

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 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:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.020
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6081
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   9436  Z= 0.141
  Angle     :  0.593   9.075  12764  Z= 0.314
  Chirality :  0.040   0.179   1371
  Planarity :  0.003   0.054   1606
  Dihedral  : 14.647  88.910   3275
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.25), residues: 1151
  helix:  1.23 (0.19), residues: 770
  sheet: -0.36 (1.84), residues: 10
  loop : -0.46 (0.35), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 157 
 TYR   0.018   0.001   TYR B 306 
 PHE   0.028   0.001   PHE B 220 
 TRP   0.030   0.001   TRP C 222 
 HIS   0.005   0.001   HIS C 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9436)
  covalent geometry    : angle       0.59336 (12764)
  hydrogen bonds       : bond        0.12725 (  595)
  hydrogen bonds       : angle       5.25136 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: B  298 MET cc_start: 0.5694 (mmp) cc_final: 0.5417 (mmp)
REVERT: B  454 TRP cc_start: 0.5900 (m100) cc_final: 0.5261 (m-10)
REVERT: B  470 ASP cc_start: 0.8060 (m-30) cc_final: 0.7800 (m-30)
REVERT: B  596 MET cc_start: 0.7095 (ppp) cc_final: 0.6822 (ppp)
REVERT: C  324 MET cc_start: 0.2572 (mtp) cc_final: 0.2284 (mtp)
REVERT: C  457 MET cc_start: 0.6210 (tmm) cc_final: 0.5987 (tmm)
REVERT: C  464 LEU cc_start: 0.7313 (mm) cc_final: 0.7049 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0705
  time to fit residues: 18.0749
Evaluate side-chains
  148 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   30.0000
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    8.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 612 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 = 0.5156 r_free = 0.5156 target = 0.271388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.225988 restraints weight = 13768.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.4754 rms_B_bonded: 3.07
r_work: 0.4539 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.4539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6419
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9436  Z= 0.131
  Angle     :  0.580  10.717  12764  Z= 0.296
  Chirality :  0.039   0.134   1371
  Planarity :  0.004   0.066   1606
  Dihedral  :  4.102  16.222   1253
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.30 %
    Favored  : 88.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.25), residues: 1151
  helix:  1.36 (0.18), residues: 770
  sheet: -0.25 (1.89), residues: 10
  loop : -0.47 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 228 
 TYR   0.032   0.002   TYR B 462 
 PHE   0.021   0.001   PHE B 299 
 TRP   0.018   0.001   TRP C 222 
 HIS   0.004   0.001   HIS C 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9436)
  covalent geometry    : angle       0.57972 (12764)
  hydrogen bonds       : bond        0.04237 (  595)
  hydrogen bonds       : angle       4.31963 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 159
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 TYR cc_start: 0.7536 (t80) cc_final: 0.7209 (t80)
REVERT: B  216 MET cc_start: 0.6507 (ptp) cc_final: 0.6194 (ptp)
REVERT: B  298 MET cc_start: 0.5536 (mmp) cc_final: 0.4940 (mmp)
REVERT: B  361 PHE cc_start: 0.7575 (m-10) cc_final: 0.7340 (m-10)
REVERT: B  457 MET cc_start: 0.5366 (tpp) cc_final: 0.5148 (tpt)
REVERT: B  470 ASP cc_start: 0.8361 (m-30) cc_final: 0.8073 (m-30)
REVERT: C  260 PHE cc_start: 0.6042 (m-10) cc_final: 0.5793 (m-10)
REVERT: C  324 MET cc_start: 0.2647 (mtp) cc_final: 0.2345 (mtp)
REVERT: C  332 SER cc_start: 0.8083 (p) cc_final: 0.7673 (m)
REVERT: C  464 LEU cc_start: 0.7566 (mm) cc_final: 0.7176 (mm)
  outliers start: 8
  outliers final: 4
  residues processed: 162
  average time/residue: 0.0780
  time to fit residues: 18.8478
Evaluate side-chains
  153 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 149
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain C residue  655 LEU
Chi-restraints excluded: chain C residue  665 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 64 optimal weight:    0.4980
   chunk 88 optimal weight:    0.4980
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B 476 GLN
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5129 r_free = 0.5129 target = 0.267767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.220828 restraints weight = 13683.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.4710 rms_B_bonded: 3.33
r_work: 0.4474 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.4474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6552
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9436  Z= 0.173
  Angle     :  0.621  11.529  12764  Z= 0.317
  Chirality :  0.040   0.142   1371
  Planarity :  0.004   0.066   1606
  Dihedral  :  4.241  19.680   1253
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.59 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.25), residues: 1151
  helix:  1.19 (0.18), residues: 768
  sheet: -0.04 (1.92), residues: 10
  loop : -0.52 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 157 
 TYR   0.027   0.002   TYR B 169 
 PHE   0.020   0.002   PHE C 704 
 TRP   0.028   0.002   TRP C 222 
 HIS   0.006   0.001   HIS C 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9436)
  covalent geometry    : angle       0.62104 (12764)
  hydrogen bonds       : bond        0.04445 (  595)
  hydrogen bonds       : angle       4.40932 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 TYR cc_start: 0.7574 (t80) cc_final: 0.7262 (t80)
REVERT: B  216 MET cc_start: 0.6693 (ptp) cc_final: 0.6450 (ptp)
REVERT: B  298 MET cc_start: 0.6040 (mmp) cc_final: 0.5783 (mmp)
REVERT: B  312 TRP cc_start: 0.6965 (t60) cc_final: 0.6417 (t60)
REVERT: B  372 MET cc_start: 0.8320 (mpp) cc_final: 0.8117 (mpp)
REVERT: B  640 PHE cc_start: 0.5985 (t80) cc_final: 0.5540 (t80)
REVERT: B  686 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8145 (t80)
REVERT: C  161 HIS cc_start: 0.5488 (OUTLIER) cc_final: 0.4479 (t-90)
REVERT: C  317 HIS cc_start: 0.7018 (t70) cc_final: 0.6703 (t70)
REVERT: C  324 MET cc_start: 0.2836 (mtp) cc_final: 0.2542 (mtp)
REVERT: C  464 LEU cc_start: 0.7666 (mm) cc_final: 0.7287 (mm)
  outliers start: 15
  outliers final: 11
  residues processed: 155
  average time/residue: 0.0808
  time to fit residues: 18.3733
Evaluate side-chains
  153 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  446 ILE
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  686 PHE
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  636 CYS
Chi-restraints excluded: chain C residue  655 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 110 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 101 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 94 optimal weight:   20.0000
   chunk 59 optimal weight:    0.9990
   chunk 112 optimal weight:    4.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C 233 GLN
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5139 r_free = 0.5139 target = 0.269342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.222478 restraints weight = 13842.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.4724 rms_B_bonded: 3.21
r_work: 0.4504 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.4504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6488
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9436  Z= 0.138
  Angle     :  0.582  10.957  12764  Z= 0.297
  Chirality :  0.039   0.147   1371
  Planarity :  0.004   0.067   1606
  Dihedral  :  4.180  19.460   1253
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.76 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.25), residues: 1151
  helix:  1.31 (0.18), residues: 771
  sheet: -0.08 (1.92), residues: 10
  loop : -0.49 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 157 
 TYR   0.029   0.002   TYR B 169 
 PHE   0.025   0.001   PHE B 435 
 TRP   0.019   0.001   TRP C 222 
 HIS   0.005   0.001   HIS C 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9436)
  covalent geometry    : angle       0.58234 (12764)
  hydrogen bonds       : bond        0.04080 (  595)
  hydrogen bonds       : angle       4.30457 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 TYR cc_start: 0.7306 (t80) cc_final: 0.7013 (t80)
REVERT: B  212 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.6865 (t80)
REVERT: B  216 MET cc_start: 0.6622 (ptp) cc_final: 0.6367 (ptp)
REVERT: B  298 MET cc_start: 0.6102 (mmp) cc_final: 0.5812 (mmp)
REVERT: B  686 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8040 (t80)
REVERT: C  161 HIS cc_start: 0.5530 (OUTLIER) cc_final: 0.4433 (t-90)
REVERT: C  317 HIS cc_start: 0.6937 (t70) cc_final: 0.6629 (t70)
REVERT: C  324 MET cc_start: 0.2788 (mtp) cc_final: 0.2499 (mtp)
REVERT: C  364 ASN cc_start: 0.6624 (p0) cc_final: 0.6416 (p0)
REVERT: C  464 LEU cc_start: 0.7657 (mm) cc_final: 0.7249 (mm)
REVERT: C  599 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6799 (t80)
  outliers start: 20
  outliers final: 10
  residues processed: 161
  average time/residue: 0.0791
  time to fit residues: 18.6063
Evaluate side-chains
  157 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  686 PHE
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  471 MET
Chi-restraints excluded: chain C residue  599 PHE
Chi-restraints excluded: chain C residue  655 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   chunk 106 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 78 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 96 optimal weight:   30.0000
   chunk 94 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 63 optimal weight:    0.4980
   overall best weight:    3.6988

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

Flipped N/Q/H residues before XYZ refinement:
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 401 HIS
C 568 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.258430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.211028 restraints weight = 13112.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.4523 rms_B_bonded: 4.29
r_work: 0.4170 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.077   9436  Z= 0.334
  Angle     :  0.837  13.787  12764  Z= 0.434
  Chirality :  0.047   0.168   1371
  Planarity :  0.006   0.068   1606
  Dihedral  :  4.908  24.813   1253
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.71 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.24), residues: 1151
  helix:  0.17 (0.18), residues: 765
  sheet:  0.05 (1.97), residues: 10
  loop : -0.60 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 262 
 TYR   0.032   0.003   TYR B 169 
 PHE   0.029   0.003   PHE C 468 
 TRP   0.041   0.003   TRP B 222 
 HIS   0.010   0.002   HIS C 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00747 ( 9436)
  covalent geometry    : angle       0.83698 (12764)
  hydrogen bonds       : bond        0.05836 (  595)
  hydrogen bonds       : angle       5.15139 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 TYR cc_start: 0.7468 (t80) cc_final: 0.7169 (t80)
REVERT: B  261 CYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6661 (t)
REVERT: B  681 LYS cc_start: 0.8692 (mttm) cc_final: 0.7538 (tptm)
REVERT: B  686 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8120 (t80)
REVERT: C  161 HIS cc_start: 0.5725 (OUTLIER) cc_final: 0.4616 (t-90)
REVERT: C  262 ARG cc_start: 0.7220 (tpp-160) cc_final: 0.7014 (tpp-160)
REVERT: C  317 HIS cc_start: 0.7105 (t70) cc_final: 0.6831 (t-90)
REVERT: C  324 MET cc_start: 0.3354 (mtp) cc_final: 0.3078 (mtp)
REVERT: C  364 ASN cc_start: 0.6809 (p0) cc_final: 0.6564 (p0)
REVERT: C  366 LYS cc_start: 0.7836 (tttt) cc_final: 0.7591 (mtpp)
REVERT: C  464 LEU cc_start: 0.7953 (mm) cc_final: 0.7565 (mm)
REVERT: C  599 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6786 (t80)
  outliers start: 28
  outliers final: 19
  residues processed: 162
  average time/residue: 0.0847
  time to fit residues: 19.7993
Evaluate side-chains
  161 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  446 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  686 PHE
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  273 ILE
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  599 PHE
Chi-restraints excluded: chain C residue  603 LEU
Chi-restraints excluded: chain C residue  636 CYS
Chi-restraints excluded: chain C residue  655 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 88 optimal weight:    0.2980
   chunk 61 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 35 optimal weight:   20.0000
   chunk 13 optimal weight:    3.9990
   chunk 97 optimal weight:   30.0000
   chunk 104 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 93 optimal weight:   20.0000
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 476 GLN
** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 568 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5079 r_free = 0.5079 target = 0.266632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.206179 restraints weight = 13009.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.4492 rms_B_bonded: 2.86
r_work: 0.4345 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9436  Z= 0.138
  Angle     :  0.626  11.445  12764  Z= 0.317
  Chirality :  0.040   0.158   1371
  Planarity :  0.004   0.068   1606
  Dihedral  :  4.471  20.604   1253
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.64 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.25), residues: 1151
  helix:  0.85 (0.18), residues: 770
  sheet: -0.04 (1.96), residues: 10
  loop : -0.54 (0.35), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 157 
 TYR   0.032   0.002   TYR B 169 
 PHE   0.021   0.001   PHE B 220 
 TRP   0.023   0.001   TRP C 222 
 HIS   0.004   0.001   HIS C 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9436)
  covalent geometry    : angle       0.62641 (12764)
  hydrogen bonds       : bond        0.04369 (  595)
  hydrogen bonds       : angle       4.53997 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 TYR cc_start: 0.7335 (t80) cc_final: 0.7067 (t80)
REVERT: B  206 MET cc_start: 0.6226 (tpt) cc_final: 0.5855 (tpt)
REVERT: B  212 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7296 (t80)
REVERT: B  261 CYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6222 (t)
REVERT: B  468 PHE cc_start: 0.6779 (p90) cc_final: 0.6343 (p90)
REVERT: B  686 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.8020 (t80)
REVERT: C  148 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8396 (pp)
REVERT: C  161 HIS cc_start: 0.5569 (OUTLIER) cc_final: 0.4441 (t-90)
REVERT: C  306 TYR cc_start: 0.7685 (t80) cc_final: 0.7384 (t80)
REVERT: C  317 HIS cc_start: 0.6831 (t70) cc_final: 0.6555 (t-90)
REVERT: C  324 MET cc_start: 0.2821 (mtp) cc_final: 0.2539 (mtp)
REVERT: C  464 LEU cc_start: 0.7800 (mm) cc_final: 0.7311 (mm)
REVERT: C  599 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6897 (t80)
REVERT: C  681 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8470 (mmtp)
  outliers start: 25
  outliers final: 12
  residues processed: 169
  average time/residue: 0.0813
  time to fit residues: 19.9664
Evaluate side-chains
  165 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  227 ASP
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  686 PHE
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  273 ILE
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  599 PHE
Chi-restraints excluded: chain C residue  636 CYS
Chi-restraints excluded: chain C residue  655 LEU
Chi-restraints excluded: chain C residue  681 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 39 optimal weight:   20.0000
   chunk 70 optimal weight:    0.0470
   chunk 43 optimal weight:    0.0050
   chunk 98 optimal weight:   30.0000
   chunk 38 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.9696

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

Flipped N/Q/H residues before XYZ refinement:
B 396 HIS
** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5077 r_free = 0.5077 target = 0.266492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.205699 restraints weight = 13098.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4486 rms_B_bonded: 2.92
r_work: 0.4338 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9436  Z= 0.144
  Angle     :  0.632  12.566  12764  Z= 0.321
  Chirality :  0.040   0.169   1371
  Planarity :  0.004   0.067   1606
  Dihedral  :  4.369  21.690   1253
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.36 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.25), residues: 1151
  helix:  0.99 (0.18), residues: 771
  sheet: -0.11 (1.93), residues: 10
  loop : -0.52 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 157 
 TYR   0.030   0.002   TYR B 169 
 PHE   0.027   0.001   PHE B 439 
 TRP   0.024   0.001   TRP B 222 
 HIS   0.004   0.001   HIS C 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9436)
  covalent geometry    : angle       0.63232 (12764)
  hydrogen bonds       : bond        0.04273 (  595)
  hydrogen bonds       : angle       4.49428 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 TYR cc_start: 0.7398 (t80) cc_final: 0.7141 (t80)
REVERT: B  206 MET cc_start: 0.6140 (tpt) cc_final: 0.5785 (tpt)
REVERT: B  212 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7292 (t80)
REVERT: B  261 CYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6199 (t)
REVERT: B  298 MET cc_start: 0.5757 (mmm) cc_final: 0.5504 (mmp)
REVERT: B  686 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7931 (t80)
REVERT: C  148 LEU cc_start: 0.8761 (mm) cc_final: 0.8410 (pp)
REVERT: C  161 HIS cc_start: 0.5699 (OUTLIER) cc_final: 0.4595 (t-90)
REVERT: C  306 TYR cc_start: 0.7686 (t80) cc_final: 0.7262 (t80)
REVERT: C  317 HIS cc_start: 0.6927 (t70) cc_final: 0.6625 (t-90)
REVERT: C  324 MET cc_start: 0.2755 (mtp) cc_final: 0.2498 (mtp)
REVERT: C  464 LEU cc_start: 0.7847 (mm) cc_final: 0.7346 (mm)
REVERT: C  599 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6847 (t80)
REVERT: C  681 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8456 (mmtp)
  outliers start: 24
  outliers final: 17
  residues processed: 168
  average time/residue: 0.0869
  time to fit residues: 21.1678
Evaluate side-chains
  171 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  227 ASP
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  641 PHE
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  686 PHE
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  273 ILE
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  599 PHE
Chi-restraints excluded: chain C residue  655 LEU
Chi-restraints excluded: chain C residue  681 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 96 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 109 optimal weight:    0.8980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 612 ASN
** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5121 r_free = 0.5121 target = 0.267440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.221312 restraints weight = 13656.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.4710 rms_B_bonded: 3.58
r_work: 0.4443 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.4443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6576
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9436  Z= 0.139
  Angle     :  0.640  12.608  12764  Z= 0.324
  Chirality :  0.039   0.180   1371
  Planarity :  0.004   0.067   1606
  Dihedral  :  4.308  21.137   1253
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.88 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.25), residues: 1151
  helix:  1.06 (0.18), residues: 772
  sheet: -0.10 (1.93), residues: 10
  loop : -0.51 (0.35), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 157 
 TYR   0.030   0.002   TYR B 169 
 PHE   0.028   0.001   PHE B 184 
 TRP   0.021   0.001   TRP B 222 
 HIS   0.008   0.001   HIS B 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9436)
  covalent geometry    : angle       0.63983 (12764)
  hydrogen bonds       : bond        0.04168 (  595)
  hydrogen bonds       : angle       4.47429 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 TYR cc_start: 0.7274 (t80) cc_final: 0.7058 (t80)
REVERT: B  206 MET cc_start: 0.6228 (tpt) cc_final: 0.5874 (tpt)
REVERT: B  212 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7391 (t80)
REVERT: B  261 CYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6280 (t)
REVERT: B  298 MET cc_start: 0.6037 (mmm) cc_final: 0.5741 (mmp)
REVERT: B  468 PHE cc_start: 0.6812 (p90) cc_final: 0.6269 (p90)
REVERT: B  686 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7998 (t80)
REVERT: C  148 LEU cc_start: 0.8729 (mm) cc_final: 0.8407 (pp)
REVERT: C  161 HIS cc_start: 0.5463 (OUTLIER) cc_final: 0.4363 (t-90)
REVERT: C  298 MET cc_start: 0.7497 (mmm) cc_final: 0.7138 (mmm)
REVERT: C  306 TYR cc_start: 0.7544 (t80) cc_final: 0.7129 (t80)
REVERT: C  317 HIS cc_start: 0.6875 (t70) cc_final: 0.6577 (t-90)
REVERT: C  324 MET cc_start: 0.2677 (mtp) cc_final: 0.2427 (mtp)
REVERT: C  464 LEU cc_start: 0.7752 (mm) cc_final: 0.7285 (mm)
REVERT: C  599 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6735 (t80)
REVERT: C  658 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7544 (t80)
REVERT: C  681 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8493 (mmtp)
  outliers start: 26
  outliers final: 18
  residues processed: 166
  average time/residue: 0.0854
  time to fit residues: 20.5249
Evaluate side-chains
  174 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  227 ASP
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  641 PHE
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  686 PHE
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  599 PHE
Chi-restraints excluded: chain C residue  636 CYS
Chi-restraints excluded: chain C residue  655 LEU
Chi-restraints excluded: chain C residue  658 PHE
Chi-restraints excluded: chain C residue  681 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 378 HIS ** 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 = 0.5134 r_free = 0.5134 target = 0.268743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4845 r_free = 0.4845 target = 0.223373 restraints weight = 13669.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.4723 rms_B_bonded: 3.52
r_work: 0.4462 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.4462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9436  Z= 0.133
  Angle     :  0.635  12.978  12764  Z= 0.321
  Chirality :  0.040   0.171   1371
  Planarity :  0.004   0.067   1606
  Dihedral  :  4.238  19.879   1253
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.60 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.25), residues: 1151
  helix:  1.16 (0.18), residues: 772
  sheet: -0.13 (1.91), residues: 10
  loop : -0.50 (0.35), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 157 
 TYR   0.029   0.001   TYR B 169 
 PHE   0.041   0.001   PHE B 184 
 TRP   0.020   0.001   TRP B 222 
 HIS   0.010   0.001   HIS B 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9436)
  covalent geometry    : angle       0.63498 (12764)
  hydrogen bonds       : bond        0.04061 (  595)
  hydrogen bonds       : angle       4.42358 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 TYR cc_start: 0.7240 (t80) cc_final: 0.7040 (t80)
REVERT: B  206 MET cc_start: 0.6261 (tpt) cc_final: 0.5907 (tpt)
REVERT: B  212 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7556 (t80)
REVERT: B  261 CYS cc_start: 0.6545 (OUTLIER) cc_final: 0.6270 (t)
REVERT: B  295 TRP cc_start: 0.7563 (m100) cc_final: 0.7132 (m100)
REVERT: B  298 MET cc_start: 0.5915 (mmm) cc_final: 0.5475 (mmp)
REVERT: B  468 PHE cc_start: 0.6814 (p90) cc_final: 0.6248 (p90)
REVERT: B  686 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7962 (t80)
REVERT: C  148 LEU cc_start: 0.8732 (mm) cc_final: 0.8408 (pp)
REVERT: C  161 HIS cc_start: 0.5556 (OUTLIER) cc_final: 0.4430 (t-90)
REVERT: C  306 TYR cc_start: 0.7546 (t80) cc_final: 0.7120 (t80)
REVERT: C  317 HIS cc_start: 0.6864 (t70) cc_final: 0.6555 (t70)
REVERT: C  324 MET cc_start: 0.2645 (mtp) cc_final: 0.2404 (mtp)
REVERT: C  464 LEU cc_start: 0.7765 (mm) cc_final: 0.7269 (mm)
REVERT: C  599 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6771 (t80)
REVERT: C  658 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7545 (t80)
REVERT: C  681 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8505 (mmtp)
  outliers start: 27
  outliers final: 19
  residues processed: 171
  average time/residue: 0.0883
  time to fit residues: 21.8157
Evaluate side-chains
  177 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  227 ASP
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  641 PHE
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  686 PHE
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  471 MET
Chi-restraints excluded: chain C residue  599 PHE
Chi-restraints excluded: chain C residue  636 CYS
Chi-restraints excluded: chain C residue  655 LEU
Chi-restraints excluded: chain C residue  658 PHE
Chi-restraints excluded: chain C residue  681 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 112 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0970
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 378 HIS ** 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 = 0.5121 r_free = 0.5121 target = 0.267013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.221417 restraints weight = 13205.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.4718 rms_B_bonded: 3.34
r_work: 0.4467 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.4467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6559
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9436  Z= 0.141
  Angle     :  0.660  12.505  12764  Z= 0.331
  Chirality :  0.040   0.175   1371
  Planarity :  0.004   0.067   1606
  Dihedral  :  4.234  19.446   1253
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.49 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1151
  helix:  1.15 (0.18), residues: 772
  sheet: -0.14 (1.91), residues: 10
  loop : -0.50 (0.35), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 157 
 TYR   0.031   0.001   TYR B 169 
 PHE   0.041   0.001   PHE B 184 
 TRP   0.017   0.001   TRP B 222 
 HIS   0.012   0.001   HIS B 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9436)
  covalent geometry    : angle       0.65992 (12764)
  hydrogen bonds       : bond        0.04147 (  595)
  hydrogen bonds       : angle       4.44984 ( 1779)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  206 MET cc_start: 0.6244 (tpt) cc_final: 0.5859 (tpt)
REVERT: B  212 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7540 (t80)
REVERT: B  261 CYS cc_start: 0.6539 (OUTLIER) cc_final: 0.6275 (t)
REVERT: B  295 TRP cc_start: 0.7564 (m100) cc_final: 0.7141 (m100)
REVERT: B  298 MET cc_start: 0.5987 (mmm) cc_final: 0.5630 (mmp)
REVERT: B  451 MET cc_start: 0.6829 (mmp) cc_final: 0.6099 (ptm)
REVERT: B  468 PHE cc_start: 0.6759 (p90) cc_final: 0.6185 (p90)
REVERT: B  686 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7957 (t80)
REVERT: C  148 LEU cc_start: 0.8709 (mm) cc_final: 0.8400 (pp)
REVERT: C  161 HIS cc_start: 0.5494 (OUTLIER) cc_final: 0.4356 (t-90)
REVERT: C  306 TYR cc_start: 0.7464 (t80) cc_final: 0.7165 (t80)
REVERT: C  317 HIS cc_start: 0.6871 (t70) cc_final: 0.6553 (t70)
REVERT: C  324 MET cc_start: 0.2626 (mtp) cc_final: 0.2385 (mtp)
REVERT: C  464 LEU cc_start: 0.7711 (mm) cc_final: 0.7235 (mm)
REVERT: C  599 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6751 (t80)
REVERT: C  658 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7579 (t80)
REVERT: C  681 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8512 (mmtp)
  outliers start: 30
  outliers final: 21
  residues processed: 164
  average time/residue: 0.0835
  time to fit residues: 19.7171
Evaluate side-chains
  175 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  227 ASP
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  641 PHE
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  683 THR
Chi-restraints excluded: chain B residue  686 PHE
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  471 MET
Chi-restraints excluded: chain C residue  599 PHE
Chi-restraints excluded: chain C residue  636 CYS
Chi-restraints excluded: chain C residue  655 LEU
Chi-restraints excluded: chain C residue  658 PHE
Chi-restraints excluded: chain C residue  681 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 80 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 94 optimal weight:   20.0000
   chunk 76 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9980
   chunk 111 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 378 HIS ** 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 = 0.5141 r_free = 0.5141 target = 0.269872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4855 r_free = 0.4855 target = 0.224772 restraints weight = 13654.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.4737 rms_B_bonded: 3.54
r_work: 0.4471 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.4471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6512
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9436  Z= 0.133
  Angle     :  0.653  12.438  12764  Z= 0.328
  Chirality :  0.040   0.191   1371
  Planarity :  0.004   0.067   1606
  Dihedral  :  4.162  18.957   1253
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.70 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.25), residues: 1151
  helix:  1.24 (0.18), residues: 772
  sheet: -0.15 (1.90), residues: 10
  loop : -0.48 (0.35), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 157 
 TYR   0.029   0.001   TYR B 169 
 PHE   0.042   0.001   PHE B 184 
 TRP   0.013   0.001   TRP B 222 
 HIS   0.017   0.001   HIS B 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9436)
  covalent geometry    : angle       0.65279 (12764)
  hydrogen bonds       : bond        0.04090 (  595)
  hydrogen bonds       : angle       4.39696 ( 1779)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2609.80 seconds
wall clock time: 45 minutes 23.46 seconds (2723.46 seconds total)