Starting phenix.real_space_refine
on Mon Apr  6 03:30:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uxl_64586/04_2026/9uxl_64586.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uxl_64586/04_2026/9uxl_64586.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uxl_64586/04_2026/9uxl_64586.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uxl_64586/04_2026/9uxl_64586.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uxl_64586/04_2026/9uxl_64586.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uxl_64586/04_2026/9uxl_64586.map"
  }
  resolution = 4.07
  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=   0.000 sd=   0.002
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      31      5.16       5
     C    9501      2.51       5
     N    2598      2.21       5
     O    2875      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15005
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 653, 5265
          Classifications: {'peptide': 653}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 628}
    Chain: "D"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1359
          Classifications: {'peptide': 170}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 160}
    Chain: "F"
      Number of atoms: 5265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 653, 5265
          Classifications: {'peptide': 653}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 628}
    Chain: "C"
      Number of atoms: 3116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3116
          Classifications: {'peptide': 385}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 376}
          Chain breaks: 1
  Time building chain proxies: 3.15, per 1000 atoms: 0.21
  Number of scatterers: 15005
  At special positions: 0
  Unit cell: (95.12, 109.88, 186.96, 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      31     16.00
     O    2875      8.00
     N    2598      7.00
     C    9501      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: 1.22
  Conformation dependent library (CDL) restraints added in 633.5 milliseconds
  

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3590

  Finding SS restraints...
    Secondary structure from input PDB file:
      84 helices and 10 sheets defined
      63.6% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 41
      No H-bonds generated for 'chain 'A' and resid 39 through 41'
    Processing helix  chain 'A' and resid 42 through 51
    Processing helix  chain 'A' and resid 61 through 66
      removed outlier: 3.587A  pdb=" N   ASP A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 130
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 3.848A  pdb=" N   LEU A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 166
      removed outlier: 3.647A  pdb=" N   ALA A 166 " --> pdb=" O   GLN A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 192
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 196 through 228
    Processing helix  chain 'A' and resid 228 through 244
      removed outlier: 4.129A  pdb=" N   SER A 232 " --> pdb=" O   GLU A 228 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   SER A 233 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 271
    Processing helix  chain 'A' and resid 278 through 317
    Processing helix  chain 'A' and resid 322 through 326
      removed outlier: 3.574A  pdb=" N   ALA A 326 " --> pdb=" O   HIS A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 342
    Processing helix  chain 'A' and resid 343 through 348
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 4.178A  pdb=" N   ILE A 357 " --> pdb=" O   GLU A 353 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ARG A 358 " --> pdb=" O   PRO A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 376
    Processing helix  chain 'A' and resid 386 through 416
    Processing helix  chain 'A' and resid 424 through 441
      removed outlier: 4.034A  pdb=" N   SER A 440 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU A 441 " --> pdb=" O   LYS A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 467
    Processing helix  chain 'A' and resid 470 through 493
      removed outlier: 3.508A  pdb=" N   TRP A 492 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 528
    Processing helix  chain 'A' and resid 530 through 552
    Processing helix  chain 'A' and resid 566 through 570
    Processing helix  chain 'A' and resid 572 through 577
      removed outlier: 4.171A  pdb=" N   ARG A 576 " --> pdb=" O   PRO A 572 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   HIS A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 572 through 577'
    Processing helix  chain 'A' and resid 581 through 592
    Processing helix  chain 'A' and resid 594 through 612
    Processing helix  chain 'A' and resid 626 through 631
    Processing helix  chain 'A' and resid 649 through 653
      removed outlier: 3.937A  pdb=" N   LEU A 653 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 16
    Processing helix  chain 'D' and resid 17 through 37
    Processing helix  chain 'D' and resid 41 through 47
      removed outlier: 3.659A  pdb=" N   LEU D  45 " --> pdb=" O   HIS D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 53
    Processing helix  chain 'D' and resid 54 through 64
      removed outlier: 4.063A  pdb=" N   VAL D  60 " --> pdb=" O   ASP D  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 77
      removed outlier: 3.677A  pdb=" N   PHE D  75 " --> pdb=" O   TYR D  71 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER D  76 " --> pdb=" O   LEU D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 110
      removed outlier: 3.893A  pdb=" N   ILE D  89 " --> pdb=" O   ILE D  85 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   HIS D  90 " --> pdb=" O   PRO D  86 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   PHE D  91 " --> pdb=" O   LEU D  87 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ASP D  94 " --> pdb=" O   HIS D  90 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   ASN D  98 " --> pdb=" O   ASP D  94 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   LYS D  99 " --> pdb=" O   ILE D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 136
    Processing helix  chain 'D' and resid 137 through 156
    Processing helix  chain 'D' and resid 158 through 166
    Processing helix  chain 'F' and resid 42 through 51
    Processing helix  chain 'F' and resid 61 through 66
    Processing helix  chain 'F' and resid 118 through 130
    Processing helix  chain 'F' and resid 143 through 147
    Processing helix  chain 'F' and resid 150 through 155
    Processing helix  chain 'F' and resid 161 through 166
      removed outlier: 4.102A  pdb=" N   ALA F 166 " --> pdb=" O   GLN F 162 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 177 through 192
      Proline residue:  F 189  - end of helix
    Processing helix  chain 'F' and resid 196 through 227
    Processing helix  chain 'F' and resid 230 through 245
    Processing helix  chain 'F' and resid 257 through 271
    Processing helix  chain 'F' and resid 274 through 277
    Processing helix  chain 'F' and resid 278 through 285
    Processing helix  chain 'F' and resid 286 through 334
    Processing helix  chain 'F' and resid 335 through 347
      removed outlier: 4.512A  pdb=" N   TRP F 339 " --> pdb=" O   SER F 335 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 356 through 361
    Processing helix  chain 'F' and resid 361 through 376
      removed outlier: 3.755A  pdb=" N   GLU F 373 " --> pdb=" O   PHE F 369 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   ALA F 374 " --> pdb=" O   SER F 370 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLU F 375 " --> pdb=" O   ASN F 371 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 379 through 416
    Processing helix  chain 'F' and resid 417 through 422
    Processing helix  chain 'F' and resid 424 through 440
    Processing helix  chain 'F' and resid 445 through 469
    Processing helix  chain 'F' and resid 470 through 491
    Processing helix  chain 'F' and resid 492 through 496
    Processing helix  chain 'F' and resid 524 through 528
      removed outlier: 3.929A  pdb=" N   ILE F 528 " --> pdb=" O   LEU F 525 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 530 through 552
    Processing helix  chain 'F' and resid 566 through 570
      removed outlier: 3.764A  pdb=" N   VAL F 569 " --> pdb=" O   PRO F 566 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 581 through 591
    Processing helix  chain 'F' and resid 594 through 612
    Processing helix  chain 'F' and resid 626 through 631
      removed outlier: 3.752A  pdb=" N   LYS F 630 " --> pdb=" O   SER F 626 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 649 through 653
    Processing helix  chain 'C' and resid 4 through 29
      removed outlier: 4.384A  pdb=" N   ALA C   8 " --> pdb=" O   ASN C   4 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 87
      removed outlier: 3.947A  pdb=" N   TRP C  74 " --> pdb=" O   SER C  70 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY C  87 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 114
    Processing helix  chain 'C' and resid 117 through 132
    Processing helix  chain 'C' and resid 139 through 148
    Processing helix  chain 'C' and resid 149 through 159
      removed outlier: 3.558A  pdb=" N   LYS C 159 " --> pdb=" O   ARG C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 181
    Processing helix  chain 'C' and resid 188 through 208
    Processing helix  chain 'C' and resid 209 through 211
      No H-bonds generated for 'chain 'C' and resid 209 through 211'
    Processing helix  chain 'C' and resid 219 through 246
    Processing helix  chain 'C' and resid 259 through 268
      removed outlier: 3.788A  pdb=" N   ILE C 268 " --> pdb=" O   GLN C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 296
      removed outlier: 3.589A  pdb=" N   LEU C 275 " --> pdb=" O   ASP C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 325
      removed outlier: 3.861A  pdb=" N   TYR C 303 " --> pdb=" O   GLN C 299 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 300 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 345
    Processing helix  chain 'C' and resid 356 through 370
    Processing helix  chain 'C' and resid 378 through 384
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
      removed outlier: 5.307A  pdb=" N   ILE A   5 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   LYS A  75 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TRP A  69 " --> pdb=" O   TRP A  11 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ARG A  86 " --> pdb=" O   ASN A  96 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   ASN A  96 " --> pdb=" O   ARG A  86 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160
      removed outlier: 7.891A  pdb=" N   GLN A 160 " --> pdb=" O   ASP A 564 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ILE A 561 " --> pdb=" O   ILE A 619 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   LEU A 621 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   TYR A 563 " --> pdb=" O   LEU A 621 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLY A  34 " --> pdb=" O   ASP A 622 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   VAL A  29 " --> pdb=" O   HIS A 636 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL A 638 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   LEU A  31 " --> pdb=" O   VAL A 638 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   GLU A 640 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   THR A  33 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 330
      removed outlier: 3.549A  pdb=" N   VAL A 382 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 508
    Processing sheet with id=AA5, first strand: chain 'D' and resid 113 through 115
    Processing sheet with id=AA6, first strand: chain 'F' and resid 20 through 23
      removed outlier: 7.056A  pdb=" N   ILE F   5 " --> pdb=" O   ILE F  74 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ILE F  74 " --> pdb=" O   ILE F   5 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   LYS F   7 " --> pdb=" O   VAL F  72 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   VAL F  72 " --> pdb=" O   LYS F   7 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   VAL F   9 " --> pdb=" O   TYR F  70 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   TYR F  70 " --> pdb=" O   VAL F   9 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   TRP F  11 " --> pdb=" O   ALA F  68 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   ARG F  86 " --> pdb=" O   ASN F  96 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   ASN F  96 " --> pdb=" O   ARG F  86 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 159 through 160
      removed outlier: 6.409A  pdb=" N   ASN F  30 " --> pdb=" O   VAL F 620 " (cutoff:3.500A)
      removed outlier: 9.221A  pdb=" N   VAL F  29 " --> pdb=" O   LEU F 637 " (cutoff:3.500A)
      removed outlier: 9.564A  pdb=" N   GLU F 639 " --> pdb=" O   VAL F  29 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   LEU F  31 " --> pdb=" O   GLU F 639 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   TRP F 641 " --> pdb=" O   LEU F  31 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   THR F  33 " --> pdb=" O   TRP F 641 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 505 through 508
    Processing sheet with id=AA9, first strand: chain 'C' and resid 160 through 163
      removed outlier: 5.706A  pdb=" N   PHE C  96 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ILE C 163 " --> pdb=" O   PHE C  96 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   LEU C  98 " --> pdb=" O   ILE C 163 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   LEU C  97 " --> pdb=" O   SER C  51 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   PHE C  53 " --> pdb=" O   LEU C  97 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   PHE C  99 " --> pdb=" O   PHE C  53 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   GLN C  55 " --> pdb=" O   PHE C  99 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   VAL C 216 " --> pdb=" O   THR C  52 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 349 through 350

    890 hydrogen bonds defined for protein.
    2577 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.83

  Time building geometry restraints manager: 1.58 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2555
        1.32 -     1.44: 3854
        1.44 -     1.57: 8824
        1.57 -     1.69: 1
        1.69 -     1.81: 49
  Bond restraints: 15283
  Sorted by residual:
  bond pdb=" N   ASP F 229 "
       pdb=" CA  ASP F 229 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.29e-02 6.01e+03 9.07e+00
  bond pdb=" N   ASN F 227 "
       pdb=" CA  ASN F 227 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.10e-02 8.26e+03 8.89e+00
  bond pdb=" CG  PRO D 130 "
       pdb=" CD  PRO D 130 "
    ideal  model  delta    sigma   weight residual
    1.503  1.407  0.096 3.40e-02 8.65e+02 7.94e+00
  bond pdb=" N   LEU F 441 "
       pdb=" CA  LEU F 441 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.033 1.29e-02 6.01e+03 6.61e+00
  bond pdb=" N   SER C 166 "
       pdb=" CA  SER C 166 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.24e-02 6.50e+03 6.38e+00
  ... (remaining 15278 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 20338
        2.52 -     5.04: 268
        5.04 -     7.57: 36
        7.57 -    10.09: 12
       10.09 -    12.61: 2
  Bond angle restraints: 20656
  Sorted by residual:
  angle pdb=" C   ARG C 224 "
        pdb=" N   LEU C 225 "
        pdb=" CA  LEU C 225 "
      ideal   model   delta    sigma   weight residual
     120.72  109.26   11.46 1.67e+00 3.59e-01 4.71e+01
  angle pdb=" N   ALA C 218 "
        pdb=" CA  ALA C 218 "
        pdb=" C   ALA C 218 "
      ideal   model   delta    sigma   weight residual
     110.06  119.38   -9.32 1.43e+00 4.89e-01 4.25e+01
  angle pdb=" N   GLU F 210 "
        pdb=" CA  GLU F 210 "
        pdb=" CB  GLU F 210 "
      ideal   model   delta    sigma   weight residual
     110.16  118.22   -8.06 1.48e+00 4.57e-01 2.97e+01
  angle pdb=" N   PRO D 130 "
        pdb=" CD  PRO D 130 "
        pdb=" CG  PRO D 130 "
      ideal   model   delta    sigma   weight residual
     103.20   95.36    7.84 1.50e+00 4.44e-01 2.73e+01
  angle pdb=" CA  PRO D 130 "
        pdb=" N   PRO D 130 "
        pdb=" CD  PRO D 130 "
      ideal   model   delta    sigma   weight residual
     112.00  104.93    7.07 1.40e+00 5.10e-01 2.55e+01
  ... (remaining 20651 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.19: 8530
       16.19 -    32.39: 710
       32.39 -    48.58: 137
       48.58 -    64.78: 20
       64.78 -    80.97: 11
  Dihedral angle restraints: 9408
    sinusoidal: 3901
      harmonic: 5507
  Sorted by residual:
  dihedral pdb=" CA  THR C  47 "
           pdb=" C   THR C  47 "
           pdb=" N   GLY C  48 "
           pdb=" CA  GLY C  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  131.85   48.15     0      5.00e+00 4.00e-02 9.27e+01
  dihedral pdb=" CA  ILE C 215 "
           pdb=" C   ILE C 215 "
           pdb=" N   VAL C 216 "
           pdb=" CA  VAL C 216 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.52   35.48     0      5.00e+00 4.00e-02 5.03e+01
  dihedral pdb=" CA  ASP C  41 "
           pdb=" C   ASP C  41 "
           pdb=" N   ASP C  42 "
           pdb=" CA  ASP C  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.62  -31.38     0      5.00e+00 4.00e-02 3.94e+01
  ... (remaining 9405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 2012
       0.065 -    0.130: 297
       0.130 -    0.194: 18
       0.194 -    0.259: 5
       0.259 -    0.324: 1
  Chirality restraints: 2333
  Sorted by residual:
  chirality pdb=" CG  LEU C 225 "
            pdb=" CB  LEU C 225 "
            pdb=" CD1 LEU C 225 "
            pdb=" CD2 LEU C 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.91    0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" CA  GLU C 127 "
            pdb=" N   GLU C 127 "
            pdb=" C   GLU C 127 "
            pdb=" CB  GLU C 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CG  LEU C  83 "
            pdb=" CB  LEU C  83 "
            pdb=" CD1 LEU C  83 "
            pdb=" CD2 LEU C  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 2330 not shown)

  Planarity restraints: 2645
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 129 "    0.075 5.00e-02 4.00e+02   1.10e-01 1.93e+01
        pdb=" N   PRO D 130 "   -0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO D 130 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO D 130 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 221 "   -0.023 2.00e-02 2.50e+03   2.27e-02 9.00e+00
        pdb=" CG  PHE C 221 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 221 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 221 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 221 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 221 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 221 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 430 "   -0.012 2.00e-02 2.50e+03   2.34e-02 5.50e+00
        pdb=" C   LYS A 430 "    0.041 2.00e-02 2.50e+03
        pdb=" O   LYS A 430 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PHE A 431 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 2642 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 300
        2.65 -     3.21: 15317
        3.21 -     3.77: 25987
        3.77 -     4.34: 34841
        4.34 -     4.90: 54339
  Nonbonded interactions: 130784
  Sorted by model distance:
  nonbonded pdb=" O   GLY D 111 "
            pdb=" ND2 ASN D 125 "
     model   vdw
     2.082 3.120
  nonbonded pdb=" OG  SER F  41 "
            pdb=" OE1 GLN F 162 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" NH1 ARG A 331 "
            pdb=" O   LYS D 167 "
     model   vdw
     2.109 3.120
  nonbonded pdb=" OG1 THR A 322 "
            pdb=" OD2 ASP A 325 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" O   SER D  64 "
            pdb=" NZ  LYS D 149 "
     model   vdw
     2.133 3.120
  ... (remaining 130779 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 'A'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.730
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     13.510
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
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      :  0.004   0.106  15283  Z= 0.214
  Angle     :  0.762  12.610  20656  Z= 0.422
  Chirality :  0.046   0.324   2333
  Planarity :  0.005   0.110   2645
  Dihedral  : 12.627  80.972   5818
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 22.92
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.00 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.24 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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 are not related in a simple way.
  whole:  1.20 (0.20), residues: 1851
  helix:  1.24 (0.16), residues: 1029
  sheet:  0.30 (0.44), residues: 139
  loop :  0.41 (0.25), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 476 
 TYR   0.012   0.002   TYR F 173 
 PHE   0.053   0.002   PHE C 221 
 TRP   0.032   0.002   TRP C  74 
 HIS   0.007   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (15283)
  covalent geometry    : angle       0.76157 (20656)
  hydrogen bonds       : bond        0.14590 (  890)
  hydrogen bonds       : angle       5.64851 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 HIS cc_start: 0.8571 (p-80) cc_final: 0.8007 (p-80)
REVERT: A  157 PHE cc_start: 0.9209 (m-80) cc_final: 0.8708 (m-80)
REVERT: A  169 ASN cc_start: 0.9359 (t0) cc_final: 0.9038 (t0)
REVERT: A  441 LEU cc_start: 0.9128 (mt) cc_final: 0.8776 (mp)
REVERT: A  602 PHE cc_start: 0.9243 (m-80) cc_final: 0.8744 (m-80)
REVERT: D   20 MET cc_start: 0.8623 (ppp) cc_final: 0.8285 (ppp)
REVERT: D   24 MET cc_start: 0.8613 (mmm) cc_final: 0.8250 (mmm)
REVERT: F  157 PHE cc_start: 0.9078 (m-80) cc_final: 0.8666 (m-80)
REVERT: C   53 PHE cc_start: 0.9217 (m-80) cc_final: 0.8907 (m-80)
REVERT: C  180 HIS cc_start: 0.9221 (t-90) cc_final: 0.8986 (t-170)
REVERT: C  284 GLU cc_start: 0.9112 (pt0) cc_final: 0.8755 (tp30)
  outliers start: 6
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1399
  time to fit residues: 23.6113
Evaluate side-chains
  72 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0470
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    0.9980
   overall best weight:    0.9880

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 226 GLN
A 311 GLN
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  34 GLN
F 281 ASN
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 344 ASN
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  46 HIS
** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.071499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.055998 restraints weight = 146416.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.057252 restraints weight = 107750.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.058167 restraints weight = 86757.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.058839 restraints weight = 73949.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.059199 restraints weight = 65603.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  15283  Z= 0.146
  Angle     :  0.609  12.378  20656  Z= 0.318
  Chirality :  0.042   0.172   2333
  Planarity :  0.004   0.043   2645
  Dihedral  :  4.817  43.294   2015
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.26 %
    Favored  : 96.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 are not related in a simple way.
  whole:  1.44 (0.20), residues: 1851
  helix:  1.53 (0.16), residues: 1041
  sheet:  0.26 (0.43), residues: 139
  loop :  0.35 (0.26), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 476 
 TYR   0.014   0.002   TYR D  33 
 PHE   0.035   0.002   PHE C 221 
 TRP   0.021   0.001   TRP F 534 
 HIS   0.008   0.001   HIS C 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (15283)
  covalent geometry    : angle       0.60927 (20656)
  hydrogen bonds       : bond        0.04459 (  890)
  hydrogen bonds       : angle       4.63002 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 HIS cc_start: 0.8197 (p-80) cc_final: 0.7583 (p-80)
REVERT: A  157 PHE cc_start: 0.9183 (m-80) cc_final: 0.8824 (m-80)
REVERT: A  169 ASN cc_start: 0.9422 (t0) cc_final: 0.8732 (t0)
REVERT: A  171 LEU cc_start: 0.7631 (mt) cc_final: 0.7163 (pt)
REVERT: A  172 PHE cc_start: 0.8818 (m-10) cc_final: 0.8445 (m-10)
REVERT: A  441 LEU cc_start: 0.9216 (mt) cc_final: 0.8933 (mp)
REVERT: A  602 PHE cc_start: 0.9211 (m-80) cc_final: 0.8696 (m-80)
REVERT: F    1 MET cc_start: 0.9402 (tmm) cc_final: 0.9100 (tmm)
REVERT: F  157 PHE cc_start: 0.9086 (m-80) cc_final: 0.8601 (m-80)
REVERT: F  303 LEU cc_start: 0.9704 (tp) cc_final: 0.9476 (pp)
REVERT: F  442 MET cc_start: 0.0906 (mmp) cc_final: 0.0651 (mmt)
REVERT: C   53 PHE cc_start: 0.9190 (m-80) cc_final: 0.8944 (m-80)
REVERT: C  180 HIS cc_start: 0.9285 (t-90) cc_final: 0.9024 (t-170)
REVERT: C  284 GLU cc_start: 0.9163 (pt0) cc_final: 0.8855 (tp30)
REVERT: C  361 HIS cc_start: 0.9437 (m-70) cc_final: 0.8702 (m-70)
  outliers start: 3
  outliers final: 3
  residues processed: 112
  average time/residue: 0.1347
  time to fit residues: 21.9027
Evaluate side-chains
  78 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 171 optimal weight:    7.9990
   chunk 161 optimal weight:    6.9990
   chunk 167 optimal weight:    8.9990
   chunk 166 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 144 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 184 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 ASN
A 495 HIS
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  34 GLN
** D  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  78 HIS
** F 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 311 GLN
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.064477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.049575 restraints weight = 159523.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.050623 restraints weight = 120191.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.051358 restraints weight = 97464.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.051898 restraints weight = 84031.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.052304 restraints weight = 75455.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.084  15283  Z= 0.316
  Angle     :  0.833  12.243  20656  Z= 0.433
  Chirality :  0.048   0.248   2333
  Planarity :  0.006   0.077   2645
  Dihedral  :  5.509  43.944   2015
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 29.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  5.46 %
    Favored  : 94.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 are not related in a simple way.
  whole:  0.38 (0.19), residues: 1851
  helix:  0.64 (0.15), residues: 1040
  sheet: -0.38 (0.45), residues: 123
  loop : -0.00 (0.25), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F 358 
 TYR   0.024   0.003   TYR A 139 
 PHE   0.028   0.003   PHE C 221 
 TRP   0.020   0.003   TRP C  74 
 HIS   0.013   0.002   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00653 (15283)
  covalent geometry    : angle       0.83330 (20656)
  hydrogen bonds       : bond        0.05153 (  890)
  hydrogen bonds       : angle       5.21817 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 HIS cc_start: 0.9422 (t-90) cc_final: 0.9134 (t-90)
REVERT: A  169 ASN cc_start: 0.9438 (t0) cc_final: 0.9007 (t0)
REVERT: A  171 LEU cc_start: 0.7698 (mt) cc_final: 0.7190 (pt)
REVERT: A  172 PHE cc_start: 0.9007 (m-10) cc_final: 0.8396 (m-10)
REVERT: A  441 LEU cc_start: 0.9323 (mt) cc_final: 0.8844 (mp)
REVERT: A  442 MET cc_start: 0.8448 (mmm) cc_final: 0.8091 (mmm)
REVERT: A  602 PHE cc_start: 0.9310 (m-80) cc_final: 0.8984 (m-80)
REVERT: D    1 MET cc_start: 0.5607 (tmm) cc_final: 0.5308 (tmm)
REVERT: D   20 MET cc_start: 0.8649 (ppp) cc_final: 0.8367 (ppp)
REVERT: D   46 PHE cc_start: 0.7967 (m-80) cc_final: 0.7767 (m-80)
REVERT: F   40 LYS cc_start: 0.5722 (OUTLIER) cc_final: 0.3647 (mtmm)
REVERT: F  311 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8788 (pp30)
REVERT: F  442 MET cc_start: 0.2683 (mmp) cc_final: 0.2466 (mmp)
  outliers start: 6
  outliers final: 2
  residues processed: 104
  average time/residue: 0.1195
  time to fit residues: 18.2822
Evaluate side-chains
  74 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 175 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 9 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 184 optimal weight:    8.9990
   chunk 106 optimal weight:   10.0000
   chunk 71 optimal weight:    0.8980
   chunk 161 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 ASN
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 623 HIS
** D  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.066659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.051526 restraints weight = 154779.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.052669 restraints weight = 114741.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.053504 restraints weight = 91739.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.054056 restraints weight = 78241.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.054545 restraints weight = 69860.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  15283  Z= 0.169
  Angle     :  0.644   8.574  20656  Z= 0.337
  Chirality :  0.043   0.191   2333
  Planarity :  0.005   0.055   2645
  Dihedral  :  5.145  45.259   2015
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 are not related in a simple way.
  whole:  0.85 (0.20), residues: 1851
  helix:  1.05 (0.16), residues: 1044
  sheet: -0.08 (0.48), residues: 117
  loop :  0.11 (0.25), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 214 
 TYR   0.023   0.002   TYR C 305 
 PHE   0.024   0.002   PHE F 172 
 TRP   0.044   0.002   TRP F 534 
 HIS   0.006   0.001   HIS C 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (15283)
  covalent geometry    : angle       0.64422 (20656)
  hydrogen bonds       : bond        0.04360 (  890)
  hydrogen bonds       : angle       4.87651 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 HIS cc_start: 0.9419 (t-90) cc_final: 0.9161 (t-90)
REVERT: A  114 HIS cc_start: 0.8257 (p-80) cc_final: 0.7560 (p90)
REVERT: A  169 ASN cc_start: 0.9388 (t0) cc_final: 0.8959 (t0)
REVERT: A  171 LEU cc_start: 0.7616 (mt) cc_final: 0.7158 (pt)
REVERT: A  172 PHE cc_start: 0.8948 (m-10) cc_final: 0.8409 (m-10)
REVERT: A  602 PHE cc_start: 0.9290 (m-80) cc_final: 0.8795 (m-80)
REVERT: D   20 MET cc_start: 0.8611 (ppp) cc_final: 0.8360 (ppp)
REVERT: D   46 PHE cc_start: 0.8135 (m-80) cc_final: 0.7841 (m-10)
REVERT: F    1 MET cc_start: 0.9249 (tmm) cc_final: 0.8975 (tmm)
REVERT: F  442 MET cc_start: 0.1786 (mmp) cc_final: 0.1496 (mmp)
REVERT: C  109 LEU cc_start: 0.8532 (tp) cc_final: 0.8251 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1378
  time to fit residues: 19.7507
Evaluate side-chains
  71 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 119 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 139 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 159 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 16 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 410 GLN
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 352 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.067712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.052492 restraints weight = 153050.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.053796 restraints weight = 112657.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.054605 restraints weight = 89325.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.055204 restraints weight = 75783.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.055543 restraints weight = 67278.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  15283  Z= 0.136
  Angle     :  0.608  10.003  20656  Z= 0.315
  Chirality :  0.042   0.159   2333
  Planarity :  0.004   0.054   2645
  Dihedral  :  4.913  43.517   2015
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.55 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 are not related in a simple way.
  whole:  1.12 (0.20), residues: 1851
  helix:  1.24 (0.16), residues: 1050
  sheet:  0.14 (0.48), residues: 117
  loop :  0.26 (0.26), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 214 
 TYR   0.017   0.001   TYR C 305 
 PHE   0.021   0.002   PHE C 221 
 TRP   0.027   0.001   TRP F 534 
 HIS   0.010   0.001   HIS C 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (15283)
  covalent geometry    : angle       0.60756 (20656)
  hydrogen bonds       : bond        0.04104 (  890)
  hydrogen bonds       : angle       4.65658 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 HIS cc_start: 0.9153 (t-90) cc_final: 0.8730 (t-90)
REVERT: A  169 ASN cc_start: 0.9364 (t0) cc_final: 0.8907 (t0)
REVERT: A  171 LEU cc_start: 0.7516 (mt) cc_final: 0.7154 (pt)
REVERT: A  172 PHE cc_start: 0.8895 (m-10) cc_final: 0.8381 (m-10)
REVERT: A  602 PHE cc_start: 0.9267 (m-80) cc_final: 0.8755 (m-80)
REVERT: D   20 MET cc_start: 0.8533 (ppp) cc_final: 0.8313 (ppp)
REVERT: D   46 PHE cc_start: 0.8136 (m-80) cc_final: 0.7794 (m-10)
REVERT: F  442 MET cc_start: 0.1655 (mmp) cc_final: 0.1333 (mmp)
REVERT: F  534 TRP cc_start: 0.8596 (m-90) cc_final: 0.7786 (m-90)
  outliers start: 1
  outliers final: 1
  residues processed: 101
  average time/residue: 0.1263
  time to fit residues: 19.0479
Evaluate side-chains
  77 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 122 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 130 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 141 optimal weight:    9.9990
   chunk 170 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 167 optimal weight:    0.1980
   chunk 30 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 202 ASN
** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.065421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.050537 restraints weight = 155135.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.051623 restraints weight = 116124.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.052386 restraints weight = 94036.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.052982 restraints weight = 80670.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.053399 restraints weight = 72109.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  15283  Z= 0.197
  Angle     :  0.665   9.677  20656  Z= 0.344
  Chirality :  0.044   0.193   2333
  Planarity :  0.005   0.054   2645
  Dihedral  :  5.042  45.495   2015
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 22.35
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.38 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 are not related in a simple way.
  whole:  0.99 (0.20), residues: 1851
  helix:  1.12 (0.16), residues: 1059
  sheet:  0.05 (0.49), residues: 118
  loop :  0.22 (0.26), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 214 
 TYR   0.014   0.002   TYR D  33 
 PHE   0.030   0.002   PHE C 221 
 TRP   0.044   0.002   TRP F 534 
 HIS   0.009   0.001   HIS A 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (15283)
  covalent geometry    : angle       0.66529 (20656)
  hydrogen bonds       : bond        0.04319 (  890)
  hydrogen bonds       : angle       4.79245 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ILE cc_start: 0.9008 (mm) cc_final: 0.8575 (tp)
REVERT: A  154 LEU cc_start: 0.8551 (mt) cc_final: 0.8164 (mp)
REVERT: A  157 PHE cc_start: 0.9386 (m-80) cc_final: 0.8801 (m-80)
REVERT: A  169 ASN cc_start: 0.9375 (t0) cc_final: 0.8859 (t0)
REVERT: A  171 LEU cc_start: 0.7662 (mt) cc_final: 0.7377 (pt)
REVERT: A  172 PHE cc_start: 0.8987 (m-10) cc_final: 0.8317 (m-10)
REVERT: A  602 PHE cc_start: 0.9313 (m-80) cc_final: 0.8823 (m-80)
REVERT: D   20 MET cc_start: 0.8570 (ppp) cc_final: 0.8299 (ppp)
REVERT: D   46 PHE cc_start: 0.8226 (m-80) cc_final: 0.7810 (m-80)
REVERT: F  442 MET cc_start: 0.2035 (mmp) cc_final: 0.1697 (mmp)
REVERT: C  109 LEU cc_start: 0.8483 (tp) cc_final: 0.8276 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1217
  time to fit residues: 17.1113
Evaluate side-chains
  66 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 144 optimal weight:    4.9990
   chunk 180 optimal weight:    7.9990
   chunk 129 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 171 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 153 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.065110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.050161 restraints weight = 153185.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.051269 restraints weight = 114049.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.052067 restraints weight = 91620.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.052681 restraints weight = 78227.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.053115 restraints weight = 69558.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  15283  Z= 0.187
  Angle     :  0.665   9.669  20656  Z= 0.343
  Chirality :  0.044   0.182   2333
  Planarity :  0.005   0.086   2645
  Dihedral  :  5.079  44.481   2015
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 20.69
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.94 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 are not related in a simple way.
  whole:  0.94 (0.20), residues: 1851
  helix:  1.07 (0.15), residues: 1051
  sheet:  0.02 (0.50), residues: 118
  loop :  0.21 (0.26), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 214 
 TYR   0.013   0.002   TYR F 213 
 PHE   0.028   0.002   PHE C 221 
 TRP   0.035   0.002   TRP F 534 
 HIS   0.009   0.001   HIS A 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (15283)
  covalent geometry    : angle       0.66467 (20656)
  hydrogen bonds       : bond        0.04287 (  890)
  hydrogen bonds       : angle       4.84766 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ILE cc_start: 0.8976 (mm) cc_final: 0.8580 (tp)
REVERT: A  154 LEU cc_start: 0.8698 (mt) cc_final: 0.8159 (mp)
REVERT: A  157 PHE cc_start: 0.9380 (m-80) cc_final: 0.8734 (m-80)
REVERT: A  158 ASN cc_start: 0.9127 (m110) cc_final: 0.8627 (m110)
REVERT: A  171 LEU cc_start: 0.7659 (mt) cc_final: 0.7414 (pt)
REVERT: A  172 PHE cc_start: 0.8943 (m-10) cc_final: 0.8263 (m-10)
REVERT: A  442 MET cc_start: 0.8770 (mmp) cc_final: 0.8461 (mmp)
REVERT: A  475 GLU cc_start: 0.9441 (mp0) cc_final: 0.9108 (pp20)
REVERT: A  602 PHE cc_start: 0.9306 (m-80) cc_final: 0.8834 (m-80)
REVERT: D   20 MET cc_start: 0.8539 (ppp) cc_final: 0.8273 (ppp)
REVERT: F  442 MET cc_start: 0.2228 (mmp) cc_final: 0.1888 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1264
  time to fit residues: 17.9403
Evaluate side-chains
  68 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   chunk 161 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 162 optimal weight:    9.9990
   chunk 70 optimal weight:    0.5980
   chunk 171 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 99 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.065741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.050665 restraints weight = 151838.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.051824 restraints weight = 111755.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.052694 restraints weight = 89840.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.053315 restraints weight = 76413.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.053710 restraints weight = 67777.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  15283  Z= 0.150
  Angle     :  0.641   9.080  20656  Z= 0.331
  Chirality :  0.044   0.178   2333
  Planarity :  0.004   0.053   2645
  Dihedral  :  4.961  43.828   2015
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 18.67
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.00 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 are not related in a simple way.
  whole:  1.11 (0.20), residues: 1851
  helix:  1.18 (0.16), residues: 1053
  sheet:  0.28 (0.50), residues: 116
  loop :  0.29 (0.26), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 214 
 TYR   0.013   0.001   TYR D 145 
 PHE   0.027   0.002   PHE C 221 
 TRP   0.037   0.002   TRP C  74 
 HIS   0.007   0.001   HIS A 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (15283)
  covalent geometry    : angle       0.64069 (20656)
  hydrogen bonds       : bond        0.04122 (  890)
  hydrogen bonds       : angle       4.76643 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ILE cc_start: 0.8936 (mm) cc_final: 0.8516 (tp)
REVERT: A  154 LEU cc_start: 0.8696 (mt) cc_final: 0.8164 (mp)
REVERT: A  157 PHE cc_start: 0.9395 (m-80) cc_final: 0.8756 (m-80)
REVERT: A  158 ASN cc_start: 0.9037 (m110) cc_final: 0.7735 (m110)
REVERT: A  172 PHE cc_start: 0.8942 (m-10) cc_final: 0.8341 (m-10)
REVERT: A  560 TYR cc_start: 0.8127 (p90) cc_final: 0.7280 (p90)
REVERT: A  602 PHE cc_start: 0.9304 (m-80) cc_final: 0.8821 (m-80)
REVERT: D    1 MET cc_start: 0.6213 (tmm) cc_final: 0.5989 (tmm)
REVERT: D   20 MET cc_start: 0.8564 (ppp) cc_final: 0.8318 (ppp)
REVERT: F  442 MET cc_start: 0.2124 (mmp) cc_final: 0.1775 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1227
  time to fit residues: 18.2818
Evaluate side-chains
  69 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 115 optimal weight:    3.9990
   chunk 172 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 136 optimal weight:    2.9990
   chunk 160 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0020
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.066820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.051697 restraints weight = 151420.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.052896 restraints weight = 111317.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.053739 restraints weight = 89101.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.054298 restraints weight = 75850.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.054816 restraints weight = 67382.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  15283  Z= 0.128
  Angle     :  0.623  10.150  20656  Z= 0.321
  Chirality :  0.043   0.245   2333
  Planarity :  0.004   0.052   2645
  Dihedral  :  4.809  42.771   2015
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.19 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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 are not related in a simple way.
  whole:  1.29 (0.20), residues: 1851
  helix:  1.33 (0.16), residues: 1054
  sheet:  0.09 (0.48), residues: 126
  loop :  0.43 (0.26), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 214 
 TYR   0.016   0.001   TYR C 164 
 PHE   0.026   0.002   PHE C 221 
 TRP   0.033   0.001   TRP C  74 
 HIS   0.009   0.001   HIS C 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (15283)
  covalent geometry    : angle       0.62260 (20656)
  hydrogen bonds       : bond        0.03989 (  890)
  hydrogen bonds       : angle       4.62384 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 LEU cc_start: 0.8700 (mt) cc_final: 0.8281 (mp)
REVERT: A  157 PHE cc_start: 0.9393 (m-80) cc_final: 0.8855 (m-80)
REVERT: A  442 MET cc_start: 0.8514 (mmp) cc_final: 0.8234 (mmp)
REVERT: A  602 PHE cc_start: 0.9326 (m-80) cc_final: 0.8868 (m-80)
REVERT: D    1 MET cc_start: 0.6688 (tmm) cc_final: 0.6417 (tmm)
REVERT: D   20 MET cc_start: 0.8602 (ppp) cc_final: 0.8336 (ppp)
REVERT: F  172 PHE cc_start: 0.9374 (m-80) cc_final: 0.9121 (m-80)
REVERT: F  442 MET cc_start: 0.1940 (mmp) cc_final: 0.1577 (mmp)
REVERT: C  357 ASP cc_start: 0.8743 (t0) cc_final: 0.8334 (t0)
REVERT: C  361 HIS cc_start: 0.9438 (m-70) cc_final: 0.8937 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1129
  time to fit residues: 17.8104
Evaluate side-chains
  77 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 129 optimal weight:    0.9980
   chunk 154 optimal weight:    0.9990
   chunk 160 optimal weight:    0.9990
   chunk 116 optimal weight:    6.9990
   chunk 136 optimal weight:    5.9990
   chunk 133 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 178 optimal weight:    6.9990
   chunk 147 optimal weight:    8.9990
   chunk 71 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 577 HIS
** F 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.066627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.051603 restraints weight = 151491.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.052803 restraints weight = 110708.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.053576 restraints weight = 88079.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.054163 restraints weight = 74990.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.054447 restraints weight = 66745.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.4027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  15283  Z= 0.133
  Angle     :  0.619  10.212  20656  Z= 0.320
  Chirality :  0.043   0.204   2333
  Planarity :  0.004   0.053   2645
  Dihedral  :  4.755  42.160   2015
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.30 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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 are not related in a simple way.
  whole:  1.33 (0.20), residues: 1851
  helix:  1.37 (0.16), residues: 1054
  sheet:  0.16 (0.49), residues: 124
  loop :  0.41 (0.26), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 214 
 TYR   0.014   0.001   TYR D  32 
 PHE   0.024   0.002   PHE C 221 
 TRP   0.030   0.001   TRP C  74 
 HIS   0.010   0.001   HIS A 577 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (15283)
  covalent geometry    : angle       0.61901 (20656)
  hydrogen bonds       : bond        0.04012 (  890)
  hydrogen bonds       : angle       4.58249 ( 2577)

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

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

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3702 Ramachandran restraints generated.
    1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ILE cc_start: 0.8882 (mm) cc_final: 0.8388 (tp)
REVERT: A  114 HIS cc_start: 0.8357 (p-80) cc_final: 0.7788 (p90)
REVERT: A  154 LEU cc_start: 0.8651 (mt) cc_final: 0.8179 (mp)
REVERT: A  157 PHE cc_start: 0.9340 (m-80) cc_final: 0.8775 (m-80)
REVERT: A  171 LEU cc_start: 0.7531 (pt) cc_final: 0.7039 (pt)
REVERT: A  602 PHE cc_start: 0.9296 (m-80) cc_final: 0.8828 (m-80)
REVERT: D    1 MET cc_start: 0.6594 (tmm) cc_final: 0.6117 (tmm)
REVERT: D   20 MET cc_start: 0.8558 (ppp) cc_final: 0.8285 (ppp)
REVERT: F  442 MET cc_start: 0.1878 (mmp) cc_final: 0.1504 (mmp)
REVERT: C   98 LEU cc_start: 0.9757 (tt) cc_final: 0.9455 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1242
  time to fit residues: 18.7746
Evaluate side-chains
  73 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 102 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0060
   chunk 16 optimal weight:    3.9990
   chunk 99 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 55 optimal weight:   10.0000
   chunk 75 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 117 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.067153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.052163 restraints weight = 151020.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.053376 restraints weight = 109614.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.054247 restraints weight = 87397.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.054918 restraints weight = 74113.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.055305 restraints weight = 65454.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  15283  Z= 0.121
  Angle     :  0.600   9.610  20656  Z= 0.309
  Chirality :  0.043   0.209   2333
  Planarity :  0.004   0.052   2645
  Dihedral  :  4.624  41.390   2015
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.13 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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 are not related in a simple way.
  whole:  1.44 (0.20), residues: 1851
  helix:  1.42 (0.16), residues: 1061
  sheet:  0.31 (0.47), residues: 130
  loop :  0.51 (0.26), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 214 
 TYR   0.017   0.001   TYR D  32 
 PHE   0.021   0.001   PHE C 221 
 TRP   0.029   0.001   TRP C  74 
 HIS   0.006   0.001   HIS C 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (15283)
  covalent geometry    : angle       0.60027 (20656)
  hydrogen bonds       : bond        0.03887 (  890)
  hydrogen bonds       : angle       4.50167 ( 2577)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3109.89 seconds
wall clock time: 54 minutes 39.39 seconds (3279.39 seconds total)