Starting phenix.real_space_refine
on Thu Jul 31 06:13:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pty_13643/07_2025/7pty_13643.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pty_13643/07_2025/7pty_13643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pty_13643/07_2025/7pty_13643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pty_13643/07_2025/7pty_13643.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pty_13643/07_2025/7pty_13643.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pty_13643/07_2025/7pty_13643.cif"
  }
  resolution = 4.63
  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
-------------------------------------------------------------------------------
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=   0.000
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      33      5.16       5
     C    8522      2.51       5
     N    2267      2.21       5
     O    2611      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13433
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 850, 6663
          Classifications: {'peptide': 850}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 25, 'TRANS': 824}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 6770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 865, 6770
          Classifications: {'peptide': 865}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 26, 'TRANS': 838}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 22
  Time building chain proxies: 9.05, per 1000 atoms: 0.67
  Number of scatterers: 13433
  At special positions: 0
  Unit cell: (142.2, 102.6, 137.7, 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      33     16.00
     O    2611      8.00
     N    2267      7.00
     C    8522      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: 3.67
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3260

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 2 sheets defined
      64.7% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 64
      removed outlier: 3.709A  pdb=" N   ILE A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 90
      Proline residue:  A  80  - end of helix
    Processing helix  chain 'A' and resid 94 through 98
    Processing helix  chain 'A' and resid 107 through 122
    Processing helix  chain 'A' and resid 131 through 160
      removed outlier: 3.679A  pdb=" N   THR A 148 " --> pdb=" O   THR A 144 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLU A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ASN A 155 " --> pdb=" O   GLU A 151 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU A 160 " --> pdb=" O   PHE A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 190
      removed outlier: 3.615A  pdb=" N   LYS A 190 " --> pdb=" O   ARG A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 215
      removed outlier: 3.903A  pdb=" N   GLU A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN A 204 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   GLY A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE A 207 " --> pdb=" O   GLU A 203 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLU A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 236
    Processing helix  chain 'A' and resid 247 through 281
      removed outlier: 3.905A  pdb=" N   GLN A 281 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 307
    Processing helix  chain 'A' and resid 312 through 326
      removed outlier: 3.722A  pdb=" N   ASN A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 353
      removed outlier: 4.082A  pdb=" N   LYS A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 432
      removed outlier: 3.956A  pdb=" N   VAL A 431 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ASP A 432 " --> pdb=" O   VAL A 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 428 through 432'
    Processing helix  chain 'A' and resid 461 through 475
      removed outlier: 4.588A  pdb=" N   ILE A 465 " --> pdb=" O   ASN A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 492
      removed outlier: 3.606A  pdb=" N   ILE A 489 " --> pdb=" O   ALA A 485 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLU A 490 " --> pdb=" O   THR A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 513
      removed outlier: 4.992A  pdb=" N   VAL A 509 " --> pdb=" O   ALA A 505 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA A 510 " --> pdb=" O   MET A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 523
      removed outlier: 4.094A  pdb=" N   LEU A 519 " --> pdb=" O   ASN A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 548
      removed outlier: 3.550A  pdb=" N   ILE A 543 " --> pdb=" O   THR A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 558
    Processing helix  chain 'A' and resid 573 through 582
    Processing helix  chain 'A' and resid 583 through 593
      removed outlier: 3.526A  pdb=" N   VAL A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   SER A 593 " --> pdb=" O   ASN A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 616
      removed outlier: 3.503A  pdb=" N   THR A 611 " --> pdb=" O   THR A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 626
      removed outlier: 3.955A  pdb=" N   LEU A 623 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 649
    Processing helix  chain 'A' and resid 650 through 661
    Processing helix  chain 'A' and resid 673 through 682
      removed outlier: 3.590A  pdb=" N   PHE A 677 " --> pdb=" O   ALA A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 694
      removed outlier: 3.600A  pdb=" N   LYS A 694 " --> pdb=" O   LEU A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 718
    Processing helix  chain 'A' and resid 719 through 728
    Processing helix  chain 'A' and resid 738 through 742
    Processing helix  chain 'A' and resid 743 through 752
    Processing helix  chain 'A' and resid 753 through 764
    Processing helix  chain 'A' and resid 776 through 783
      removed outlier: 3.839A  pdb=" N   ILE A 780 " --> pdb=" O   THR A 776 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   MET A 783 " --> pdb=" O   HIS A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 797
    Processing helix  chain 'A' and resid 809 through 818
      removed outlier: 3.519A  pdb=" N   GLY A 818 " --> pdb=" O   ALA A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 829
      removed outlier: 3.620A  pdb=" N   VAL A 823 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 851
    Processing helix  chain 'A' and resid 852 through 862
    Processing helix  chain 'A' and resid 875 through 883
    Processing helix  chain 'A' and resid 885 through 894
      removed outlier: 3.552A  pdb=" N   VAL A 889 " --> pdb=" O   ASP A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 907
    Processing helix  chain 'A' and resid 908 through 916
    Processing helix  chain 'A' and resid 922 through 927
      removed outlier: 4.118A  pdb=" N   PHE A 926 " --> pdb=" O   LEU A 922 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 65
      removed outlier: 3.542A  pdb=" N   GLY B  65 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 89
      Proline residue:  B  80  - end of helix
    Processing helix  chain 'B' and resid 108 through 122
      removed outlier: 3.786A  pdb=" N   ILE B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 131
      No H-bonds generated for 'chain 'B' and resid 129 through 131'
    Processing helix  chain 'B' and resid 132 through 159
      removed outlier: 4.001A  pdb=" N   THR B 144 " --> pdb=" O   LYS B 140 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL B 145 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLU B 154 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 162
      No H-bonds generated for 'chain 'B' and resid 160 through 162'
    Processing helix  chain 'B' and resid 167 through 190
      removed outlier: 3.949A  pdb=" N   ILE B 171 " --> pdb=" O   GLU B 167 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN B 187 " --> pdb=" O   GLU B 183 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ARG B 188 " --> pdb=" O   LYS B 184 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE B 189 " --> pdb=" O   GLU B 185 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   LYS B 190 " --> pdb=" O   ARG B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 213
      removed outlier: 4.237A  pdb=" N   GLU B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLN B 204 " --> pdb=" O   LYS B 200 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS B 205 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLY B 206 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ILE B 207 " --> pdb=" O   GLU B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 236
      removed outlier: 4.036A  pdb=" N   ASP B 231 " --> pdb=" O   ASN B 227 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   TYR B 236 " --> pdb=" O   LYS B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 281
      removed outlier: 4.108A  pdb=" N   TYR B 252 " --> pdb=" O   PHE B 248 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA B 253 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 327
      removed outlier: 4.076A  pdb=" N   ASN B 289 " --> pdb=" O   ASP B 285 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA B 290 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 351
    Processing helix  chain 'B' and resid 352 through 355
      removed outlier: 4.315A  pdb=" N   ILE B 355 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 352 through 355'
    Processing helix  chain 'B' and resid 428 through 432
      removed outlier: 3.628A  pdb=" N   VAL B 431 " --> pdb=" O   LYS B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 474
    Processing helix  chain 'B' and resid 477 through 490
    Processing helix  chain 'B' and resid 503 through 513
      removed outlier: 3.516A  pdb=" N   HIS B 507 " --> pdb=" O   ARG B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 522
    Processing helix  chain 'B' and resid 525 through 532
      removed outlier: 3.712A  pdb=" N   LEU B 532 " --> pdb=" O   ILE B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 546
      removed outlier: 4.240A  pdb=" N   GLU B 546 " --> pdb=" O   HIS B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 559
      removed outlier: 4.053A  pdb=" N   HIS B 559 " --> pdb=" O   LEU B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 580
      removed outlier: 4.317A  pdb=" N   ARG B 580 " --> pdb=" O   HIS B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 593
      removed outlier: 3.819A  pdb=" N   ARG B 588 " --> pdb=" O   SER B 584 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   ASN B 589 " --> pdb=" O   LYS B 585 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LEU B 590 " --> pdb=" O   THR B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 613
    Processing helix  chain 'B' and resid 617 through 626
      removed outlier: 3.935A  pdb=" N   ASP B 621 " --> pdb=" O   TYR B 617 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ASN B 625 " --> pdb=" O   ASP B 621 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   HIS B 626 " --> pdb=" O   ALA B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 649
    Processing helix  chain 'B' and resid 650 through 661
    Processing helix  chain 'B' and resid 673 through 682
      removed outlier: 4.268A  pdb=" N   PHE B 677 " --> pdb=" O   ALA B 673 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ALA B 678 " --> pdb=" O   PRO B 674 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA B 679 " --> pdb=" O   ILE B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 694
      removed outlier: 3.772A  pdb=" N   LYS B 694 " --> pdb=" O   LEU B 690 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 701
      removed outlier: 3.935A  pdb=" N   ILE B 699 " --> pdb=" O   LYS B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 717
      removed outlier: 3.772A  pdb=" N   PHE B 713 " --> pdb=" O   THR B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 728
    Processing helix  chain 'B' and resid 743 through 752
    Processing helix  chain 'B' and resid 753 through 763
    Processing helix  chain 'B' and resid 776 through 784
    Processing helix  chain 'B' and resid 787 through 796
      removed outlier: 3.935A  pdb=" N   VAL B 791 " --> pdb=" O   PRO B 787 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 809 through 818
    Processing helix  chain 'B' and resid 819 through 829
    Processing helix  chain 'B' and resid 842 through 851
      removed outlier: 3.543A  pdb=" N   LEU B 846 " --> pdb=" O   THR B 842 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 852 through 862
    Processing helix  chain 'B' and resid 875 through 884
    Processing helix  chain 'B' and resid 885 through 895
      removed outlier: 4.160A  pdb=" N   GLU B 894 " --> pdb=" O   ARG B 890 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LYS B 895 " --> pdb=" O   LEU B 891 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 904 through 906
      No H-bonds generated for 'chain 'B' and resid 904 through 906'
    Processing helix  chain 'B' and resid 907 through 916
      removed outlier: 3.647A  pdb=" N   ILE B 911 " --> pdb=" O   GLY B 907 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 920 through 927
    Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 401
    Processing sheet with id=AA2, first strand: chain 'B' and resid 406 through 408
      removed outlier: 3.954A  pdb=" N   ARG B 438 " --> pdb=" O   MET B 455 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   MET B 455 " --> pdb=" O   ARG B 438 " (cutoff:3.500A)

    695 hydrogen bonds defined for protein.
    2052 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: 4.71

  Time building geometry restraints manager: 4.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4459
        1.34 -     1.46: 2794
        1.46 -     1.58: 6331
        1.58 -     1.70: 0
        1.70 -     1.82: 63
  Bond restraints: 13647
  Sorted by residual:
  bond pdb=" CA  ARG A 215 "
       pdb=" C   ARG A 215 "
    ideal  model  delta    sigma   weight residual
    1.523  1.569 -0.045 1.34e-02 5.57e+03 1.15e+01
  bond pdb=" C   CYS B 424 "
       pdb=" N   PRO B 425 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.034 2.34e-02 1.83e+03 2.12e+00
  bond pdb=" CD  GLU B 828 "
       pdb=" OE1 GLU B 828 "
    ideal  model  delta    sigma   weight residual
    1.249  1.223  0.026 1.90e-02 2.77e+03 1.88e+00
  bond pdb=" CG  GLU B 828 "
       pdb=" CD  GLU B 828 "
    ideal  model  delta    sigma   weight residual
    1.516  1.487  0.029 2.50e-02 1.60e+03 1.33e+00
  bond pdb=" C   VAL A 214 "
       pdb=" N   ARG A 215 "
    ideal  model  delta    sigma   weight residual
    1.332  1.317  0.015 1.40e-02 5.10e+03 1.16e+00
  ... (remaining 13642 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 17816
        1.61 -     3.23: 501
        3.23 -     4.84: 101
        4.84 -     6.46: 26
        6.46 -     8.07: 3
  Bond angle restraints: 18447
  Sorted by residual:
  angle pdb=" N   GLY B 191 "
        pdb=" CA  GLY B 191 "
        pdb=" C   GLY B 191 "
      ideal   model   delta    sigma   weight residual
     112.50  117.59   -5.09 1.16e+00 7.43e-01 1.93e+01
  angle pdb=" N   GLU B 828 "
        pdb=" CA  GLU B 828 "
        pdb=" CB  GLU B 828 "
      ideal   model   delta    sigma   weight residual
     110.28  116.53   -6.25 1.55e+00 4.16e-01 1.63e+01
  angle pdb=" C   LEU B 827 "
        pdb=" N   GLU B 828 "
        pdb=" CA  GLU B 828 "
      ideal   model   delta    sigma   weight residual
     120.31  114.88    5.43 1.52e+00 4.33e-01 1.28e+01
  angle pdb=" N   VAL A  77 "
        pdb=" CA  VAL A  77 "
        pdb=" C   VAL A  77 "
      ideal   model   delta    sigma   weight residual
     112.96  109.51    3.45 1.00e+00 1.00e+00 1.19e+01
  angle pdb=" C   LEU A 469 "
        pdb=" N   TYR A 470 "
        pdb=" CA  TYR A 470 "
      ideal   model   delta    sigma   weight residual
     120.31  115.39    4.92 1.52e+00 4.33e-01 1.05e+01
  ... (remaining 18442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7559
       17.96 -    35.91: 683
       35.91 -    53.87: 84
       53.87 -    71.83: 11
       71.83 -    89.78: 10
  Dihedral angle restraints: 8347
    sinusoidal: 3333
      harmonic: 5014
  Sorted by residual:
  dihedral pdb=" CA  GLU A 164 "
           pdb=" C   GLU A 164 "
           pdb=" N   SER A 165 "
           pdb=" CA  SER A 165 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.06   29.94     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  PHE A 444 "
           pdb=" C   PHE A 444 "
           pdb=" N   ASN A 445 "
           pdb=" CA  ASN A 445 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.87  -28.13     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  PHE B 156 "
           pdb=" C   PHE B 156 "
           pdb=" N   LYS B 157 "
           pdb=" CA  LYS B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.22   27.78     0      5.00e+00 4.00e-02 3.09e+01
  ... (remaining 8344 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1577
       0.043 -    0.086: 480
       0.086 -    0.129: 78
       0.129 -    0.172: 8
       0.172 -    0.216: 2
  Chirality restraints: 2145
  Sorted by residual:
  chirality pdb=" CB  ILE B 366 "
            pdb=" CA  ILE B 366 "
            pdb=" CG1 ILE B 366 "
            pdb=" CG2 ILE B 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CG  LEU A 254 "
            pdb=" CB  LEU A 254 "
            pdb=" CD1 LEU A 254 "
            pdb=" CD2 LEU A 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.25e-01
  chirality pdb=" CA  GLU B 114 "
            pdb=" N   GLU B 114 "
            pdb=" C   GLU B 114 "
            pdb=" CB  GLU B 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.19e-01
  ... (remaining 2142 not shown)

  Planarity restraints: 2382
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 448 "    0.040 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO B 449 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 216 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.78e+00
        pdb=" N   PRO A 217 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 217 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 217 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 415 "   -0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO A 416 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 416 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 416 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 2379 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1407
        2.74 -     3.28: 16436
        3.28 -     3.82: 23587
        3.82 -     4.36: 28241
        4.36 -     4.90: 42335
  Nonbonded interactions: 112006
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 511 "
            pdb=" NE2 GLN B 549 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   GLU B 725 "
            pdb=" NE2 GLN B 729 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   PHE B 462 "
            pdb=" ND1 HIS B 466 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" OG  SER B 135 "
            pdb=" OG  SER B 273 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" NE2 HIS B 779 "
            pdb=" O   LEU B 808 "
     model   vdw
     2.219 3.120
  ... (remaining 112001 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' and (resid 50 through 195 or (resid 196 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 197 through 578 or (resid 579 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 580 through 616 or (resid 6 \ 
17 and (name N or name CA or name C or name O or name CB )) or resid 618 through \ 
 928))
  selection = (chain 'B' and (resid 50 through 90 or resid 93 through 98 or resid 106 through  \ 
214 or (resid 215 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 216 through 219 or (resid 220 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 221 through 236 or resid 246 through 355 or resid 367 throug \ 
h 928))
}

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:             2.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     35.330
  Find NCS groups from input model:        0.740
  Set up NCS constraints:                  0.120
  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:4.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
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   0.045  13647  Z= 0.166
  Angle     :  0.681   8.072  18447  Z= 0.376
  Chirality :  0.041   0.216   2145
  Planarity :  0.005   0.060   2382
  Dihedral  : 13.762  89.785   5087
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 25.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.89 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.20), residues: 1699
  helix:  0.31 (0.17), residues: 971
  sheet: -3.98 (0.58), residues: 54
  loop : -2.57 (0.23), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 389 
 HIS   0.004   0.001   HIS A 466 
 PHE   0.033   0.002   PHE A 499 
 TYR   0.020   0.002   TYR A 716 
 ARG   0.005   0.000   ARG A 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12899 (  695)
  hydrogen bonds       : angle       6.34213 ( 2052)
  covalent geometry    : bond        0.00333 (13647)
  covalent geometry    : angle       0.68056 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 1.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  424 CYS cc_start: 0.8000 (m) cc_final: 0.7772 (m)
REVERT: A  686 MET cc_start: 0.8863 (mmp) cc_final: 0.8549 (mmm)
REVERT: B  686 MET cc_start: 0.9149 (mpp) cc_final: 0.8614 (mpp)
REVERT: B  888 MET cc_start: 0.8923 (mtt) cc_final: 0.8367 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.2266
  time to fit residues: 24.5299
Evaluate side-chains
  55 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 144 optimal weight:    8.9990
   chunk 129 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 134 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 99 optimal weight:    0.1980
   chunk 155 optimal weight:    0.0970
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 234 ASN
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 536 ASN
** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.044809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.036583 restraints weight = 170424.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.037429 restraints weight = 125246.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.038037 restraints weight = 99503.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13647  Z= 0.126
  Angle     :  0.596   6.698  18447  Z= 0.322
  Chirality :  0.040   0.223   2145
  Planarity :  0.004   0.055   2382
  Dihedral  :  5.755  27.629   1804
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.89 %
    Favored  : 93.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.20), residues: 1699
  helix:  0.47 (0.16), residues: 994
  sheet: -3.87 (0.60), residues: 54
  loop : -2.61 (0.22), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 389 
 HIS   0.005   0.001   HIS B 466 
 PHE   0.023   0.001   PHE B 156 
 TYR   0.020   0.002   TYR B 261 
 ARG   0.004   0.000   ARG B 784 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04392 (  695)
  hydrogen bonds       : angle       5.21726 ( 2052)
  covalent geometry    : bond        0.00261 (13647)
  covalent geometry    : angle       0.59643 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 1.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  686 MET cc_start: 0.9134 (mmp) cc_final: 0.8894 (mmm)
REVERT: B  869 TYR cc_start: 0.8579 (p90) cc_final: 0.8032 (p90)
REVERT: B  888 MET cc_start: 0.9066 (mtt) cc_final: 0.8376 (mtp)
REVERT: B  912 MET cc_start: 0.9618 (tpt) cc_final: 0.9380 (tpt)
  outliers start: 4
  outliers final: 1
  residues processed: 67
  average time/residue: 0.2140
  time to fit residues: 23.9364
Evaluate side-chains
  54 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 145 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 138 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 167 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 916 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 = 0.3444 r_free = 0.3444 target = 0.043815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.035663 restraints weight = 174741.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.036509 restraints weight = 129448.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.037116 restraints weight = 102564.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13647  Z= 0.160
  Angle     :  0.615   6.074  18447  Z= 0.334
  Chirality :  0.040   0.197   2145
  Planarity :  0.005   0.080   2382
  Dihedral  :  5.782  27.240   1804
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  4.67 %
    Favored  : 95.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.20), residues: 1699
  helix:  0.46 (0.16), residues: 996
  sheet: -4.13 (0.58), residues: 55
  loop : -2.56 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 413 
 HIS   0.005   0.001   HIS B 466 
 PHE   0.028   0.002   PHE B 156 
 TYR   0.018   0.002   TYR B 261 
 ARG   0.003   0.000   ARG A 430 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04370 (  695)
  hydrogen bonds       : angle       5.22616 ( 2052)
  covalent geometry    : bond        0.00331 (13647)
  covalent geometry    : angle       0.61524 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 1.532 
Fit side-chains
   revert: symmetry clash
REVERT: A  686 MET cc_start: 0.9149 (mmp) cc_final: 0.8903 (mmm)
REVERT: B  455 MET cc_start: 0.8199 (pmm) cc_final: 0.7999 (pmm)
REVERT: B  869 TYR cc_start: 0.8643 (p90) cc_final: 0.8031 (p90)
REVERT: B  888 MET cc_start: 0.9086 (mtt) cc_final: 0.8364 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 0.2263
  time to fit residues: 24.1483
Evaluate side-chains
  54 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 142 optimal weight:    0.8980
   chunk 129 optimal weight:    6.9990
   chunk 165 optimal weight:    0.9990
   chunk 127 optimal weight:    6.9990
   chunk 115 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 130 optimal weight:    0.9990
   chunk 157 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0060
   chunk 148 optimal weight:    5.9990
   overall best weight:    1.1802

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

Flipped N/Q/H residues before XYZ refinement:
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 450 GLN
A 526 GLN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.044943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.036653 restraints weight = 169919.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.037540 restraints weight = 125801.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.038166 restraints weight = 99450.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13647  Z= 0.123
  Angle     :  0.585   6.338  18447  Z= 0.313
  Chirality :  0.040   0.228   2145
  Planarity :  0.005   0.074   2382
  Dihedral  :  5.619  27.543   1804
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  4.06 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.20), residues: 1699
  helix:  0.57 (0.16), residues: 997
  sheet: -3.70 (0.63), residues: 47
  loop : -2.64 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 413 
 HIS   0.004   0.001   HIS A 878 
 PHE   0.022   0.001   PHE B 156 
 TYR   0.023   0.002   TYR B 261 
 ARG   0.002   0.000   ARG B 436 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  695)
  hydrogen bonds       : angle       5.01529 ( 2052)
  covalent geometry    : bond        0.00258 (13647)
  covalent geometry    : angle       0.58500 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 2.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  686 MET cc_start: 0.9133 (mmp) cc_final: 0.8875 (mmm)
REVERT: B  869 TYR cc_start: 0.8607 (p90) cc_final: 0.7850 (p90)
REVERT: B  888 MET cc_start: 0.9005 (mtt) cc_final: 0.8276 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 67
  average time/residue: 0.3885
  time to fit residues: 44.5600
Evaluate side-chains
  54 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 107 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 164 optimal weight:    7.9990
   chunk 49 optimal weight:    0.3980
   chunk 117 optimal weight:    0.0040
   chunk 102 optimal weight:    5.9990
   overall best weight:    0.7794

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** 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 = 0.3511 r_free = 0.3511 target = 0.045811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.037454 restraints weight = 168589.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.038347 restraints weight = 124508.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.038992 restraints weight = 98465.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  13647  Z= 0.116
  Angle     :  0.580   6.475  18447  Z= 0.309
  Chirality :  0.039   0.213   2145
  Planarity :  0.004   0.055   2382
  Dihedral  :  5.419  26.730   1804
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.52 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.20), residues: 1699
  helix:  0.68 (0.16), residues: 996
  sheet: -3.77 (0.63), residues: 48
  loop : -2.60 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 708 
 HIS   0.003   0.001   HIS B 812 
 PHE   0.022   0.001   PHE B 462 
 TYR   0.023   0.002   TYR B 261 
 ARG   0.004   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03925 (  695)
  hydrogen bonds       : angle       4.84629 ( 2052)
  covalent geometry    : bond        0.00235 (13647)
  covalent geometry    : angle       0.58027 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 1.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  686 MET cc_start: 0.9142 (mmp) cc_final: 0.8860 (mmm)
REVERT: B  869 TYR cc_start: 0.8488 (p90) cc_final: 0.7776 (p90)
REVERT: B  888 MET cc_start: 0.9045 (mtt) cc_final: 0.8158 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.5046
  time to fit residues: 60.4028
Evaluate side-chains
  53 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 3.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 107 optimal weight:    7.9990
   chunk 119 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 151 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 146 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 157 optimal weight:    9.9990
   chunk 1 optimal weight:    0.0050
   overall best weight:    1.6002

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 332 ASN
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.045557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.037626 restraints weight = 175311.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.038476 restraints weight = 128580.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.039147 restraints weight = 101493.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13647  Z= 0.127
  Angle     :  0.593   8.958  18447  Z= 0.317
  Chirality :  0.040   0.229   2145
  Planarity :  0.004   0.060   2382
  Dihedral  :  5.394  25.958   1804
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.20), residues: 1699
  helix:  0.81 (0.16), residues: 982
  sheet: -3.84 (0.63), residues: 48
  loop : -2.49 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 708 
 HIS   0.003   0.001   HIS B 812 
 PHE   0.024   0.002   PHE B 156 
 TYR   0.028   0.002   TYR B 261 
 ARG   0.002   0.000   ARG A 430 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  695)
  hydrogen bonds       : angle       4.89314 ( 2052)
  covalent geometry    : bond        0.00263 (13647)
  covalent geometry    : angle       0.59256 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 3.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  686 MET cc_start: 0.9106 (mmp) cc_final: 0.8812 (mmm)
REVERT: B  869 TYR cc_start: 0.8462 (p90) cc_final: 0.7746 (p90)
REVERT: B  888 MET cc_start: 0.8961 (mtt) cc_final: 0.8187 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.3139
  time to fit residues: 38.7335
Evaluate side-chains
  57 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 167 optimal weight:    3.9990
   chunk 154 optimal weight:    0.9990
   chunk 69 optimal weight:    8.9990
   chunk 85 optimal weight:   20.0000
   chunk 97 optimal weight:    0.7980
   chunk 150 optimal weight:    4.9990
   chunk 155 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 137 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.045384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.037482 restraints weight = 175587.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.038343 restraints weight = 128825.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.038991 restraints weight = 101714.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13647  Z= 0.131
  Angle     :  0.597   7.222  18447  Z= 0.318
  Chirality :  0.040   0.209   2145
  Planarity :  0.004   0.052   2382
  Dihedral  :  5.411  26.341   1804
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.20), residues: 1699
  helix:  0.85 (0.17), residues: 982
  sheet: -3.84 (0.62), residues: 48
  loop : -2.51 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 389 
 HIS   0.003   0.001   HIS A 746 
 PHE   0.023   0.001   PHE B 156 
 TYR   0.022   0.002   TYR B 261 
 ARG   0.012   0.000   ARG B 908 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (  695)
  hydrogen bonds       : angle       4.89357 ( 2052)
  covalent geometry    : bond        0.00271 (13647)
  covalent geometry    : angle       0.59725 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  686 MET cc_start: 0.9109 (mmp) cc_final: 0.8810 (mmm)
REVERT: B  265 MET cc_start: 0.8487 (mtt) cc_final: 0.8224 (mtp)
REVERT: B  869 TYR cc_start: 0.8533 (p90) cc_final: 0.7824 (p90)
REVERT: B  888 MET cc_start: 0.8922 (mtt) cc_final: 0.8054 (mtp)
REVERT: B  912 MET cc_start: 0.9588 (mmp) cc_final: 0.9303 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.2309
  time to fit residues: 28.5732
Evaluate side-chains
  53 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 132 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 126 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9990
   chunk 115 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 151 optimal weight:    0.0030
   chunk 163 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.9596

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

Flipped N/Q/H residues before XYZ refinement:
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.045135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.037226 restraints weight = 176823.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.038091 restraints weight = 129190.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.038733 restraints weight = 101626.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13647  Z= 0.138
  Angle     :  0.611   6.600  18447  Z= 0.327
  Chirality :  0.040   0.228   2145
  Planarity :  0.004   0.056   2382
  Dihedral  :  5.439  26.208   1804
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.20), residues: 1699
  helix:  0.79 (0.16), residues: 985
  sheet: -3.97 (0.60), residues: 50
  loop : -2.51 (0.22), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 389 
 HIS   0.007   0.001   HIS A 559 
 PHE   0.024   0.002   PHE B 156 
 TYR   0.021   0.002   TYR B 261 
 ARG   0.004   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  695)
  hydrogen bonds       : angle       4.97078 ( 2052)
  covalent geometry    : bond        0.00285 (13647)
  covalent geometry    : angle       0.61066 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.703 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 GLU cc_start: 0.9066 (mp0) cc_final: 0.8821 (mp0)
REVERT: A  686 MET cc_start: 0.9074 (mmp) cc_final: 0.8772 (mmm)
REVERT: B  869 TYR cc_start: 0.8497 (p90) cc_final: 0.7747 (p90)
REVERT: B  888 MET cc_start: 0.8908 (mtt) cc_final: 0.8059 (mtp)
REVERT: B  912 MET cc_start: 0.9560 (mmp) cc_final: 0.9205 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.2361
  time to fit residues: 28.7241
Evaluate side-chains
  56 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 167 optimal weight:    0.0970
   chunk 98 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 139 optimal weight:    0.5980
   chunk 91 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 168 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   chunk 2 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 807 ASN
A 861 ASN
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.046451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.037934 restraints weight = 166813.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.038824 restraints weight = 123440.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.039476 restraints weight = 98073.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13647  Z= 0.118
  Angle     :  0.602   7.163  18447  Z= 0.318
  Chirality :  0.040   0.220   2145
  Planarity :  0.004   0.050   2382
  Dihedral  :  5.264  25.996   1804
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.20), residues: 1699
  helix:  0.82 (0.16), residues: 994
  sheet: -3.87 (0.60), residues: 50
  loop : -2.52 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 708 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.021   0.001   PHE A 444 
 TYR   0.026   0.001   TYR B 261 
 ARG   0.003   0.000   ARG A 430 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03801 (  695)
  hydrogen bonds       : angle       4.80887 ( 2052)
  covalent geometry    : bond        0.00238 (13647)
  covalent geometry    : angle       0.60239 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  686 MET cc_start: 0.9103 (mmp) cc_final: 0.8821 (mmm)
REVERT: B  672 MET cc_start: 0.8930 (mpp) cc_final: 0.8712 (mpp)
REVERT: B  869 TYR cc_start: 0.8475 (p90) cc_final: 0.7750 (p90)
REVERT: B  888 MET cc_start: 0.8939 (mtt) cc_final: 0.8080 (mtp)
REVERT: B  912 MET cc_start: 0.9612 (mmp) cc_final: 0.9234 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2326
  time to fit residues: 28.9714
Evaluate side-chains
  55 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 29 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0370
   chunk 135 optimal weight:    0.3980
   chunk 43 optimal weight:    0.0970
   chunk 83 optimal weight:   10.0000
   chunk 124 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
A 461 ASN
B 249 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 861 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.047236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.038992 restraints weight = 170780.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.039882 restraints weight = 126394.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.040548 restraints weight = 99983.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13647  Z= 0.119
  Angle     :  0.599   7.349  18447  Z= 0.316
  Chirality :  0.040   0.237   2145
  Planarity :  0.004   0.052   2382
  Dihedral  :  5.075  25.556   1804
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.20), residues: 1699
  helix:  0.93 (0.17), residues: 981
  sheet: -3.87 (0.59), residues: 50
  loop : -2.40 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 708 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.021   0.001   PHE A 444 
 TYR   0.030   0.001   TYR B 261 
 ARG   0.004   0.000   ARG B 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  695)
  hydrogen bonds       : angle       4.81187 ( 2052)
  covalent geometry    : bond        0.00239 (13647)
  covalent geometry    : angle       0.59938 (18447)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 GLU cc_start: 0.9084 (mp0) cc_final: 0.8882 (pm20)
REVERT: A  686 MET cc_start: 0.9012 (mmp) cc_final: 0.8722 (mmm)
REVERT: B  869 TYR cc_start: 0.8356 (p90) cc_final: 0.7644 (p90)
REVERT: B  888 MET cc_start: 0.8964 (mtt) cc_final: 0.8173 (mtp)
REVERT: B  912 MET cc_start: 0.9587 (mmp) cc_final: 0.9212 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.2470
  time to fit residues: 30.7471
Evaluate side-chains
  56 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 143 optimal weight:    0.0070
   chunk 107 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 162 optimal weight:    8.9990
   chunk 86 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 83 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 140 optimal weight:    5.9990
   chunk 129 optimal weight:    0.9990
   overall best weight:    3.8006

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 459 GLN
A 526 GLN
A 861 ASN
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 332 ASN
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 861 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.044095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.036294 restraints weight = 178767.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.037133 restraints weight = 130792.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.037742 restraints weight = 103117.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13647  Z= 0.196
  Angle     :  0.678   7.365  18447  Z= 0.367
  Chirality :  0.042   0.189   2145
  Planarity :  0.005   0.053   2382
  Dihedral  :  5.586  26.401   1804
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.20), residues: 1699
  helix:  0.59 (0.16), residues: 979
  sheet: -4.10 (0.57), residues: 50
  loop : -2.45 (0.22), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP A 389 
 HIS   0.007   0.001   HIS B 610 
 PHE   0.027   0.002   PHE B 156 
 TYR   0.024   0.003   TYR B 261 
 ARG   0.003   0.001   ARG A 430 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  695)
  hydrogen bonds       : angle       5.17983 ( 2052)
  covalent geometry    : bond        0.00399 (13647)
  covalent geometry    : angle       0.67813 (18447)

===============================================================================
Job complete
usr+sys time: 4154.58 seconds
wall clock time: 77 minutes 35.38 seconds (4655.38 seconds total)