Starting phenix.real_space_refine
on Fri Mar 15 03:37:18 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/03_2024/8dd8_27336.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/03_2024/8dd8_27336.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/03_2024/8dd8_27336.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/03_2024/8dd8_27336.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/03_2024/8dd8_27336.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd8_27336/03_2024/8dd8_27336.pdb"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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      75      5.16       5
     C    6683      2.51       5
     N    1810      2.21       5
     O    1924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  182": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  218": "OE1" <-> "OE2"
    Residue "A TYR  432": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  469": "OE1" <-> "OE2"
    Residue "A TYR  606": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  710": "OE1" <-> "OE2"
    Residue "A GLU  791": "OE1" <-> "OE2"
    Residue "A PHE  945": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  959": "OD1" <-> "OD2"
    Residue "B GLU  342": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 10492
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1011, 8265
          Classifications: {'peptide': 1011}
          Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 963}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2227
          Classifications: {'peptide': 261}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 256}
          Chain breaks: 2
  Time building chain proxies: 5.67, per 1000 atoms: 0.54
  Number of scatterers: 10492
  At special positions: 0
  Unit cell: (89.024, 109.824, 137.28, 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      75     16.00
     O    1924      8.00
     N    1810      7.00
     C    6683      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  - 3.50
        Amino acid           : False - 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: 3.83
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2434

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 10 sheets defined
      48.6% alpha, 11.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 54
      removed outlier: 3.660A  pdb=" N   GLU A  48 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ARG A  54 " --> pdb=" O   PHE A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 62
    Processing helix  chain 'A' and resid 107 through 122
      removed outlier: 3.540A  pdb=" N   LYS A 111 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
    Processing helix  chain 'A' and resid 133 through 154
      removed outlier: 3.580A  pdb=" N   GLN A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   LEU A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   ASN A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 178 through 183
      removed outlier: 3.726A  pdb=" N   ASN A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 233
      removed outlier: 3.888A  pdb=" N   ARG A 230 " --> pdb=" O   ARG A 226 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   SER A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   MET A 232 " --> pdb=" O   LYS A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 248
      removed outlier: 3.747A  pdb=" N   VAL A 243 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LEU A 244 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLU A 245 " --> pdb=" O   CYS A 242 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   GLN A 247 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   GLY A 248 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 290 through 297
      removed outlier: 3.501A  pdb=" N   LEU A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 488 through 496
    Processing helix  chain 'A' and resid 526 through 537
      removed outlier: 3.705A  pdb=" N   GLN A 530 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ARG A 537 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
    Processing helix  chain 'A' and resid 556 through 563
      removed outlier: 3.631A  pdb=" N   VAL A 559 " --> pdb=" O   HIS A 556 " (cutoff:3.500A)
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 564 through 572
    Processing helix  chain 'A' and resid 577 through 589
      removed outlier: 3.668A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 600 through 603
    Processing helix  chain 'A' and resid 608 through 623
    Processing helix  chain 'A' and resid 624 through 631
    Processing helix  chain 'A' and resid 631 through 638
    Processing helix  chain 'A' and resid 647 through 658
    Processing helix  chain 'A' and resid 660 through 674
      removed outlier: 3.725A  pdb=" N   PHE A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLU A 674 " --> pdb=" O   HIS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
    Processing helix  chain 'A' and resid 697 through 723
      removed outlier: 4.487A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 740
    Processing helix  chain 'A' and resid 741 through 748
    Processing helix  chain 'A' and resid 807 through 828
    Processing helix  chain 'A' and resid 857 through 863
      removed outlier: 4.021A  pdb=" N   LYS A 863 " --> pdb=" O   GLN A 859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 875 through 885
    Processing helix  chain 'A' and resid 886 through 888
      No H-bonds generated for 'chain 'A' and resid 886 through 888'
    Processing helix  chain 'A' and resid 889 through 912
    Processing helix  chain 'A' and resid 957 through 965
    Processing helix  chain 'A' and resid 974 through 994
    Processing helix  chain 'A' and resid 994 through 1006
      removed outlier: 3.979A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1026
      removed outlier: 3.808A  pdb=" N   ILE A1019 " --> pdb=" O   SER A1015 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR A1021 " --> pdb=" O   ASP A1017 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A1022 " --> pdb=" O   ASP A1018 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A1026 " --> pdb=" O   ILE A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1048
      removed outlier: 3.545A  pdb=" N   LEU A1036 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 347
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 4.005A  pdb=" N   GLY B 388 " --> pdb=" O   HIS B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 411
    Processing helix  chain 'B' and resid 446 through 448
      No H-bonds generated for 'chain 'B' and resid 446 through 448'
    Processing helix  chain 'B' and resid 449 through 504
      removed outlier: 3.796A  pdb=" N   ASN B 453 " --> pdb=" O   LEU B 449 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR B 454 " --> pdb=" O   HIS B 450 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLN B 455 " --> pdb=" O   GLU B 451 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   PHE B 456 " --> pdb=" O   TYR B 452 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLN B 457 " --> pdb=" O   ASN B 453 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   GLU B 458 " --> pdb=" O   THR B 454 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LYS B 459 " --> pdb=" O   GLN B 455 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU B 462 " --> pdb=" O   GLU B 458 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA B 483 " --> pdb=" O   MET B 479 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE B 484 " --> pdb=" O   LYS B 480 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLU B 485 " --> pdb=" O   ARG B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 565
      removed outlier: 3.872A  pdb=" N   MET B 525 " --> pdb=" O   ILE B 521 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   HIS B 526 " --> pdb=" O   GLN B 522 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS B 530 " --> pdb=" O   HIS B 526 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B 531 " --> pdb=" O   ASN B 527 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU B 547 " --> pdb=" O   ARG B 543 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LYS B 550 " --> pdb=" O   GLU B 546 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   GLN B 552 " --> pdb=" O   ASP B 548 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 575
      removed outlier: 3.699A  pdb=" N   LYS B 575 " --> pdb=" O   ILE B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 578
      No H-bonds generated for 'chain 'B' and resid 576 through 578'
    Processing helix  chain 'B' and resid 593 through 598
      removed outlier: 4.263A  pdb=" N   LEU B 598 " --> pdb=" O   LEU B 594 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 36
      removed outlier: 3.709A  pdb=" N   MET A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A  34 " --> pdb=" O   VAL A  22 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   VAL A 101 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   VAL A  73 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212
      removed outlier: 4.005A  pdb=" N   GLN A 205 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   LEU A 285 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
      removed outlier: 5.880A  pdb=" N   VAL A 193 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP A 195 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   ALA A 289 " --> pdb=" O   TRP A 195 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   MET A 288 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326
      removed outlier: 6.084A  pdb=" N   LYS A 325 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392
      removed outlier: 6.853A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 477 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.594A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.594A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   SER A 408 " --> pdb=" O   PRO A 421 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752
    Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771
      removed outlier: 6.857A  pdb=" N   VAL A 845 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AB1, first strand: chain 'B' and resid 377 through 381
      removed outlier: 3.655A  pdb=" N   ASN B 377 " --> pdb=" O   LYS B 374 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   THR B 354 " --> pdb=" O   ARG B 373 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1338 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.53

  Time building geometry restraints manager: 4.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3437
        1.35 -     1.46: 2385
        1.46 -     1.58: 4776
        1.58 -     1.70: 0
        1.70 -     1.82: 117
  Bond restraints: 10715
  Sorted by residual:
  bond pdb=" CB  CYS A 901 "
       pdb=" SG  CYS A 901 "
    ideal  model  delta    sigma   weight residual
    1.808  1.772  0.036 3.30e-02 9.18e+02 1.21e+00
  bond pdb=" CG1 ILE A1022 "
       pdb=" CD1 ILE A1022 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.14e+00
  bond pdb=" CG  LEU A 327 "
       pdb=" CD1 LEU A 327 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.14e+00
  bond pdb=" CA  ILE A 197 "
       pdb=" CB  ILE A 197 "
    ideal  model  delta    sigma   weight residual
    1.540  1.553 -0.013 1.36e-02 5.41e+03 8.60e-01
  bond pdb=" CG  LEU A 929 "
       pdb=" CD2 LEU A 929 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.32e-01
  ... (remaining 10710 not shown)

  Histogram of bond angle deviations from ideal:
       97.93 -   105.15: 183
      105.15 -   112.37: 5304
      112.37 -   119.59: 3761
      119.59 -   126.80: 5047
      126.80 -   134.02: 152
  Bond angle restraints: 14447
  Sorted by residual:
  angle pdb=" CB  MET A 489 "
        pdb=" CG  MET A 489 "
        pdb=" SD  MET A 489 "
      ideal   model   delta    sigma   weight residual
     112.70  123.58  -10.88 3.00e+00 1.11e-01 1.32e+01
  angle pdb=" C   LYS B 419 "
        pdb=" N   LEU B 420 "
        pdb=" CA  LEU B 420 "
      ideal   model   delta    sigma   weight residual
     121.54  126.93   -5.39 1.91e+00 2.74e-01 7.97e+00
  angle pdb=" C   VAL A 196 "
        pdb=" N   ILE A 197 "
        pdb=" CA  ILE A 197 "
      ideal   model   delta    sigma   weight residual
     121.97  126.99   -5.02 1.80e+00 3.09e-01 7.77e+00
  angle pdb=" N   SER A 199 "
        pdb=" CA  SER A 199 "
        pdb=" C   SER A 199 "
      ideal   model   delta    sigma   weight residual
     108.07  110.28   -2.21 8.90e-01 1.26e+00 6.17e+00
  angle pdb=" C   LEU A 234 "
        pdb=" N   SER A 235 "
        pdb=" CA  SER A 235 "
      ideal   model   delta    sigma   weight residual
     121.54  126.24   -4.70 1.91e+00 2.74e-01 6.07e+00
  ... (remaining 14442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.67: 5632
       16.67 -    33.35: 716
       33.35 -    50.02: 157
       50.02 -    66.69: 32
       66.69 -    83.36: 16
  Dihedral angle restraints: 6553
    sinusoidal: 2801
      harmonic: 3752
  Sorted by residual:
  dihedral pdb=" CA  ALA A 775 "
           pdb=" C   ALA A 775 "
           pdb=" N   LYS A 776 "
           pdb=" CA  LYS A 776 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.32   17.68     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  ASP B 560 "
           pdb=" CB  ASP B 560 "
           pdb=" CG  ASP B 560 "
           pdb=" OD1 ASP B 560 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.52   57.52     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  ASP B 367 "
           pdb=" C   ASP B 367 "
           pdb=" N   TYR B 368 "
           pdb=" CA  TYR B 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.47   16.53     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 6550 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1059
       0.039 -    0.078: 372
       0.078 -    0.118: 104
       0.118 -    0.157: 22
       0.157 -    0.196: 1
  Chirality restraints: 1558
  Sorted by residual:
  chirality pdb=" CB  ILE A 197 "
            pdb=" CA  ILE A 197 "
            pdb=" CG1 ILE A 197 "
            pdb=" CG2 ILE A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.62e-01
  chirality pdb=" CA  VAL A 216 "
            pdb=" N   VAL A 216 "
            pdb=" C   VAL A 216 "
            pdb=" CB  VAL A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" CG  LEU A 956 "
            pdb=" CB  LEU A 956 "
            pdb=" CD1 LEU A 956 "
            pdb=" CD2 LEU A 956 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.73e-01
  ... (remaining 1555 not shown)

  Planarity restraints: 1854
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  16 "    0.042 5.00e-02 4.00e+02   6.29e-02 6.32e+00
        pdb=" N   PRO A  17 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A  17 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  17 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 216 "    0.040 5.00e-02 4.00e+02   6.11e-02 5.98e+00
        pdb=" N   PRO A 217 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A 217 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 217 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 420 "   -0.031 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO A 421 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 421 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 421 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1851 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1145
        2.75 -     3.29: 10361
        3.29 -     3.82: 17182
        3.82 -     4.36: 20438
        4.36 -     4.90: 35207
  Nonbonded interactions: 84333
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 970 "
            pdb=" OG1 THR A 972 "
     model   vdw
     2.211 2.440
  nonbonded pdb=" O   GLN B 497 "
            pdb=" OG1 THR B 500 "
     model   vdw
     2.221 2.440
  nonbonded pdb=" OD1 ASN A 157 "
            pdb=" OG  SER A 161 "
     model   vdw
     2.279 2.440
  nonbonded pdb=" OD2 ASP A 138 "
            pdb=" OH  TYR A 432 "
     model   vdw
     2.291 2.440
  nonbonded pdb=" NH2 ARG A 916 "
            pdb=" O   ASP A 933 "
     model   vdw
     2.292 2.520
  ... (remaining 84328 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          13.830
  Check model and map are aligned:         0.150
  Set scattering table:                    0.090
  Process input model:                     30.330
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10715  Z= 0.221
  Angle     :  0.600  10.879  14447  Z= 0.300
  Chirality :  0.044   0.196   1558
  Planarity :  0.004   0.063   1854
  Dihedral  : 15.623  83.365   4119
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.97 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.22), residues: 1258
  helix:  0.30 (0.22), residues: 520
  sheet: -0.20 (0.43), residues: 141
  loop : -1.11 (0.23), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 780 
 HIS   0.015   0.001   HIS A  47 
 PHE   0.012   0.001   PHE A 954 
 TYR   0.014   0.001   TYR B 508 
 ARG   0.003   0.000   ARG A  93 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.287 
Fit side-chains
REVERT: A  216 VAL cc_start: 0.8536 (t) cc_final: 0.8292 (t)
REVERT: A  599 MET cc_start: 0.8163 (ttp) cc_final: 0.7946 (ttp)
REVERT: A  961 LEU cc_start: 0.7271 (mm) cc_final: 0.6972 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.2340
  time to fit residues: 35.7226
Evaluate side-chains
  89 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 99 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0570
   chunk 60 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 115 optimal weight:    5.9990
   overall best weight:    0.8900

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 HIS
B 415 GLN
** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10715  Z= 0.208
  Angle     :  0.513   6.691  14447  Z= 0.269
  Chirality :  0.042   0.155   1558
  Planarity :  0.004   0.055   1854
  Dihedral  :  4.099  17.783   1393
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.58 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  5.64 %
    Favored  : 94.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.23), residues: 1258
  helix:  0.95 (0.22), residues: 549
  sheet: -0.16 (0.43), residues: 139
  loop : -1.03 (0.25), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 780 
 HIS   0.017   0.001   HIS A1048 
 PHE   0.011   0.001   PHE A 666 
 TYR   0.020   0.001   TYR A 246 
 ARG   0.002   0.000   ARG B 544 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 1.202 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 99
  average time/residue: 0.2236
  time to fit residues: 32.2927
Evaluate side-chains
  91 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 HIS
Chi-restraints excluded: chain B residue  531 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 95 optimal weight:    0.5980
   chunk 78 optimal weight:    0.3980
   chunk 31 optimal weight:    0.0970
   chunk 115 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 114 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 415 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10715  Z= 0.140
  Angle     :  0.466   7.215  14447  Z= 0.242
  Chirality :  0.041   0.159   1558
  Planarity :  0.003   0.055   1854
  Dihedral  :  3.939  17.587   1393
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  8.97 %
    Favored  : 90.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.24), residues: 1258
  helix:  1.21 (0.22), residues: 550
  sheet: -0.16 (0.43), residues: 139
  loop : -1.00 (0.25), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 780 
 HIS   0.004   0.001   HIS A 665 
 PHE   0.010   0.001   PHE A  50 
 TYR   0.014   0.001   TYR B 508 
 ARG   0.001   0.000   ARG A 975 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.995 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.7788 (mm) cc_final: 0.7570 (mt)
  outliers start: 7
  outliers final: 4
  residues processed: 105
  average time/residue: 0.2220
  time to fit residues: 33.9298
Evaluate side-chains
  98 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  875 HIS
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  531 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 114 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   chunk 55 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.2588

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

Flipped N/Q/H residues before XYZ refinement:
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN
B 415 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10715  Z= 0.264
  Angle     :  0.518   7.278  14447  Z= 0.266
  Chirality :  0.042   0.151   1558
  Planarity :  0.003   0.055   1854
  Dihedral  :  4.045  17.681   1393
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 11.54 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.24), residues: 1258
  helix:  1.18 (0.22), residues: 554
  sheet: -0.34 (0.42), residues: 139
  loop : -1.04 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 780 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.018   0.001   PHE B 456 
 TYR   0.019   0.001   TYR B 508 
 ARG   0.003   0.000   ARG A 818 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 1.318 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.7817 (mm) cc_final: 0.7584 (mt)
  outliers start: 7
  outliers final: 6
  residues processed: 95
  average time/residue: 0.2203
  time to fit residues: 30.9713
Evaluate side-chains
  96 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  875 HIS
Chi-restraints excluded: chain A residue  895 ASP
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  556 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 91 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 104 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 62 optimal weight:    2.9990
   chunk 110 optimal weight:    8.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10715  Z= 0.342
  Angle     :  0.559   6.680  14447  Z= 0.286
  Chirality :  0.044   0.149   1558
  Planarity :  0.004   0.056   1854
  Dihedral  :  4.229  18.086   1393
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.69 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 13.68 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.23), residues: 1258
  helix:  1.04 (0.22), residues: 555
  sheet: -0.58 (0.42), residues: 141
  loop : -1.08 (0.25), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 780 
 HIS   0.005   0.001   HIS A  47 
 PHE   0.022   0.002   PHE B 456 
 TYR   0.017   0.001   TYR B 508 
 ARG   0.004   0.000   ARG A 818 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 1.258 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.7882 (mm) cc_final: 0.7594 (mt)
REVERT: A  232 MET cc_start: 0.6450 (ptp) cc_final: 0.5874 (ptm)
  outliers start: 12
  outliers final: 11
  residues processed: 98
  average time/residue: 0.2206
  time to fit residues: 32.1423
Evaluate side-chains
  96 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 CYS
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  875 HIS
Chi-restraints excluded: chain A residue  895 ASP
Chi-restraints excluded: chain B residue  349 ASP
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  377 ASN
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  556 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 110 optimal weight:    0.0040
   chunk 24 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 122 optimal weight:    5.9990
   chunk 102 optimal weight:    6.9990
   chunk 56 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 917 HIS
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10715  Z= 0.163
  Angle     :  0.480   7.536  14447  Z= 0.247
  Chirality :  0.041   0.159   1558
  Planarity :  0.003   0.056   1854
  Dihedral  :  4.018  17.970   1393
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.05 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.10 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.24), residues: 1258
  helix:  1.24 (0.22), residues: 556
  sheet: -0.38 (0.42), residues: 139
  loop : -0.98 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 780 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.020   0.001   PHE B 456 
 TYR   0.016   0.001   TYR B 508 
 ARG   0.001   0.000   ARG A 141 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 1.259 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.7868 (mm) cc_final: 0.7592 (mt)
REVERT: A  232 MET cc_start: 0.6391 (ptp) cc_final: 0.5875 (ptm)
REVERT: B  450 HIS cc_start: 0.5298 (m90) cc_final: 0.5057 (m90)
  outliers start: 13
  outliers final: 9
  residues processed: 101
  average time/residue: 0.2215
  time to fit residues: 32.5975
Evaluate side-chains
  95 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  875 HIS
Chi-restraints excluded: chain A residue  895 ASP
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  556 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 68 optimal weight:    0.7980
   chunk 122 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 917 HIS
A 920 ASN
A1044 ASN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10715  Z= 0.329
  Angle     :  0.560   7.684  14447  Z= 0.285
  Chirality :  0.043   0.156   1558
  Planarity :  0.004   0.054   1854
  Dihedral  :  4.196  17.924   1393
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.01 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 15.30 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.23), residues: 1258
  helix:  1.13 (0.22), residues: 553
  sheet: -0.56 (0.43), residues: 137
  loop : -1.03 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 780 
 HIS   0.005   0.001   HIS A  47 
 PHE   0.019   0.002   PHE B 456 
 TYR   0.016   0.001   TYR B 508 
 ARG   0.003   0.000   ARG A 818 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 1.117 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.7927 (mm) cc_final: 0.7621 (mt)
REVERT: A  123 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7038 (ppp)
REVERT: A  232 MET cc_start: 0.6505 (ptp) cc_final: 0.5996 (ptm)
  outliers start: 12
  outliers final: 9
  residues processed: 94
  average time/residue: 0.2218
  time to fit residues: 30.5917
Evaluate side-chains
  95 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  875 HIS
Chi-restraints excluded: chain A residue  895 ASP
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  377 ASN
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  556 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 75 optimal weight:    0.0370
   chunk 48 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 83 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A1044 ASN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10715  Z= 0.170
  Angle     :  0.485   7.762  14447  Z= 0.249
  Chirality :  0.041   0.154   1558
  Planarity :  0.003   0.056   1854
  Dihedral  :  4.021  17.994   1393
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.05 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.04 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.24), residues: 1258
  helix:  1.32 (0.22), residues: 556
  sheet: -0.38 (0.42), residues: 139
  loop : -0.97 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.017   0.001   PHE B 456 
 TYR   0.014   0.001   TYR B 508 
 ARG   0.001   0.000   ARG A 141 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 1.210 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.7894 (mm) cc_final: 0.7610 (mt)
REVERT: A  123 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7028 (ppp)
REVERT: A  232 MET cc_start: 0.6469 (ptp) cc_final: 0.5984 (ptm)
  outliers start: 14
  outliers final: 10
  residues processed: 99
  average time/residue: 0.2047
  time to fit residues: 30.5916
Evaluate side-chains
  96 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  875 HIS
Chi-restraints excluded: chain A residue  895 ASP
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  377 ASN
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  556 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 111 optimal weight:    0.6980
   chunk 117 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 103 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10715  Z= 0.266
  Angle     :  0.537   8.331  14447  Z= 0.272
  Chirality :  0.043   0.165   1558
  Planarity :  0.003   0.054   1854
  Dihedral  :  4.087  17.817   1393
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.85 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.73 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1258
  helix:  1.24 (0.22), residues: 554
  sheet: -0.60 (0.41), residues: 149
  loop : -0.99 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 780 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.017   0.001   PHE B 456 
 TYR   0.015   0.001   TYR B 508 
 ARG   0.002   0.000   ARG A 818 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 1.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.7926 (mm) cc_final: 0.7620 (mt)
REVERT: A  123 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.6977 (ppp)
REVERT: A  232 MET cc_start: 0.6551 (ptp) cc_final: 0.6070 (ptm)
  outliers start: 13
  outliers final: 11
  residues processed: 94
  average time/residue: 0.2018
  time to fit residues: 28.6438
Evaluate side-chains
  95 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  875 HIS
Chi-restraints excluded: chain A residue  895 ASP
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  377 ASN
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  556 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 120 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   chunk 126 optimal weight:    0.0670
   chunk 116 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7122

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

Flipped N/Q/H residues before XYZ refinement:
A1044 ASN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10715  Z= 0.177
  Angle     :  0.498   8.154  14447  Z= 0.253
  Chirality :  0.041   0.158   1558
  Planarity :  0.003   0.056   1854
  Dihedral  :  3.990  17.848   1393
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.13 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 15.90 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.24), residues: 1258
  helix:  1.40 (0.22), residues: 552
  sheet: -0.28 (0.43), residues: 138
  loop : -0.93 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 780 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.017   0.001   PHE B 456 
 TYR   0.013   0.001   TYR B 508 
 ARG   0.001   0.000   ARG A 916 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7004 (ppp)
REVERT: A  232 MET cc_start: 0.6535 (ptp) cc_final: 0.6059 (ptm)
  outliers start: 12
  outliers final: 10
  residues processed: 93
  average time/residue: 0.2089
  time to fit residues: 29.3552
Evaluate side-chains
  94 residues out of total 1170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  875 HIS
Chi-restraints excluded: chain A residue  895 ASP
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  377 ASN
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  556 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 80 optimal weight:    0.3980
   chunk 107 optimal weight:    0.0010
   chunk 30 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0670
   chunk 14 optimal weight:    0.0060
   chunk 27 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 42 optimal weight:    0.2980
   chunk 103 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.1540

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 415 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.130009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.103681 restraints weight = 21709.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.34
r_work: 0.3262 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10715  Z= 0.121
  Angle     :  0.478   7.617  14447  Z= 0.244
  Chirality :  0.041   0.163   1558
  Planarity :  0.003   0.056   1854
  Dihedral  :  3.827  17.697   1393
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 16.24 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.24), residues: 1258
  helix:  1.59 (0.23), residues: 552
  sheet: -0.10 (0.43), residues: 138
  loop : -0.86 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 335 
 HIS   0.006   0.001   HIS A 665 
 PHE   0.016   0.001   PHE B 456 
 TYR   0.013   0.001   TYR B 508 
 ARG   0.002   0.000   ARG A  54 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2135.64 seconds
wall clock time: 39 minutes 25.98 seconds (2365.98 seconds total)