Starting phenix.real_space_refine (version: 1.21rc1)
on Sat Jul  8 11:21:34 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/07_2023/7mr2_23954.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/07_2023/7mr2_23954.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/07_2023/7mr2_23954.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/07_2023/7mr2_23954.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/07_2023/7mr2_23954.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/07_2023/7mr2_23954.pdb"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.003
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      80      5.16       5
     C   10553      2.51       5
     N    2927      2.21       5
     O    3111      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  277": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP 1061": "OD1" <-> "OD2"
    Residue "D PHE   23": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP   95": "OD1" <-> "OD2"
    Residue "D ASP  105": "OD1" <-> "OD2"
    Residue "D TYR  108": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib"
  Total number of atoms: 16671
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 6827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 855, 6827
          Classifications: {'peptide': 855}
          Link IDs: {'PTRANS': 34, 'TRANS': 820}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 8887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1097, 8887
          Classifications: {'peptide': 1097}
          Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1032}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 957
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 6, 'TRANS': 116}
  Time building chain proxies: 7.90, per 1000 atoms: 0.47
  Number of scatterers: 16671
  At special positions: 0
  Unit cell: (141.25, 128.82, 142.38, 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      80     16.00
     O    3111      8.00
     N    2927      7.00
     C   10553      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: 6.21
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3940

  Finding SS restraints...
    Secondary structure from input PDB file:
      92 helices and 13 sheets defined
      55.4% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'B' and resid 30 through 43
      removed outlier: 3.813A  pdb=" N   ALA B  35 " --> pdb=" O   PHE B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
    Processing helix  chain 'B' and resid 67 through 90
      removed outlier: 3.677A  pdb=" N   GLU B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 103
    Processing helix  chain 'B' and resid 106 through 119
      removed outlier: 3.886A  pdb=" N   ARG B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 124
      removed outlier: 3.798A  pdb=" N   GLU B 123 " --> pdb=" O   GLN B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 138
      removed outlier: 3.507A  pdb=" N   ASN B 138 " --> pdb=" O   GLN B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 171
      removed outlier: 4.110A  pdb=" N   LEU B 159 " --> pdb=" O   ASP B 155 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ARG B 170 " --> pdb=" O   ASP B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 187
      removed outlier: 4.221A  pdb=" N   VAL B 182 " --> pdb=" O   GLU B 178 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL B 183 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TRP B 187 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 198
    Processing helix  chain 'B' and resid 199 through 201
      No H-bonds generated for 'chain 'B' and resid 199 through 201'
    Processing helix  chain 'B' and resid 217 through 235
      removed outlier: 3.972A  pdb=" N   THR B 231 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   VAL B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 240
      removed outlier: 3.917A  pdb=" N   ALA B 239 " --> pdb=" O   GLN B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 266
      removed outlier: 3.654A  pdb=" N   ASN B 258 " --> pdb=" O   ARG B 254 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN B 262 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.931A  pdb=" N   LEU B 286 " --> pdb=" O   PRO B 283 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLU B 287 " --> pdb=" O   GLU B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 318
      removed outlier: 4.642A  pdb=" N   ASP B 314 " --> pdb=" O   PHE B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 347
      removed outlier: 4.329A  pdb=" N   THR B 329 " --> pdb=" O   ASP B 325 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLU B 334 " --> pdb=" O   ARG B 330 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ARG B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG B 344 " --> pdb=" O   ALA B 340 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ARG B 345 " --> pdb=" O   ARG B 341 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ARG B 346 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 364
      removed outlier: 3.549A  pdb=" N   LEU B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 378
      removed outlier: 3.528A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE B 374 " --> pdb=" O   LEU B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 402
    Processing helix  chain 'B' and resid 420 through 424
      removed outlier: 4.041A  pdb=" N   GLY B 424 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 435
      removed outlier: 3.813A  pdb=" N   MET B 431 " --> pdb=" O   ILE B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 462
      removed outlier: 3.586A  pdb=" N   PHE B 461 " --> pdb=" O   VAL B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 534
      removed outlier: 3.650A  pdb=" N   MET B 518 " --> pdb=" O   TYR B 514 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN B 520 " --> pdb=" O   SER B 516 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLN B 534 " --> pdb=" O   LEU B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 573
      removed outlier: 3.747A  pdb=" N   VAL B 567 " --> pdb=" O   GLU B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 589
    Processing helix  chain 'B' and resid 590 through 605
      removed outlier: 4.084A  pdb=" N   GLN B 594 " --> pdb=" O   THR B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 617
      removed outlier: 3.579A  pdb=" N   LEU B 612 " --> pdb=" O   ARG B 608 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA B 615 " --> pdb=" O   THR B 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 634
      removed outlier: 3.532A  pdb=" N   ASN B 633 " --> pdb=" O   GLU B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 656
      removed outlier: 3.567A  pdb=" N   VAL B 641 " --> pdb=" O   ALA B 637 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE B 645 " --> pdb=" O   VAL B 641 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY B 647 " --> pdb=" O   GLU B 643 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLN B 650 " --> pdb=" O   ASP B 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 657 through 669
      removed outlier: 3.511A  pdb=" N   LEU B 661 " --> pdb=" O   VAL B 657 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   MET B 665 " --> pdb=" O   LEU B 661 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG B 668 " --> pdb=" O   LEU B 664 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASN B 669 " --> pdb=" O   MET B 665 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 677
    Processing helix  chain 'B' and resid 680 through 699
      removed outlier: 3.691A  pdb=" N   ASP B 686 " --> pdb=" O   ARG B 682 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE B 687 " --> pdb=" O   ARG B 683 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 688 " --> pdb=" O   LEU B 684 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN B 695 " --> pdb=" O   SER B 691 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   GLU B 696 " --> pdb=" O   GLU B 692 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ALA B 697 " --> pdb=" O   LEU B 693 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   THR B 699 " --> pdb=" O   GLN B 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 703 through 716
      removed outlier: 3.568A  pdb=" N   VAL B 708 " --> pdb=" O   GLU B 704 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER B 712 " --> pdb=" O   VAL B 708 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU B 716 " --> pdb=" O   SER B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 725
      removed outlier: 3.705A  pdb=" N   GLN B 725 " --> pdb=" O   ALA B 722 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 783 through 806
    Processing helix  chain 'B' and resid 832 through 835
    Processing helix  chain 'B' and resid 836 through 844
      removed outlier: 3.950A  pdb=" N   ARG B 840 " --> pdb=" O   SER B 836 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU B 841 " --> pdb=" O   ALA B 837 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU B 842 " --> pdb=" O   LEU B 838 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 849 through 860
      removed outlier: 4.116A  pdb=" N   LEU B 860 " --> pdb=" O   CYS B 856 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 24
      removed outlier: 4.199A  pdb=" N   LEU C  13 " --> pdb=" O   ARG C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 55
    Processing helix  chain 'C' and resid 64 through 77
    Processing helix  chain 'C' and resid 89 through 103
      removed outlier: 3.748A  pdb=" N   TRP C  93 " --> pdb=" O   GLN C  89 " (cutoff:3.500A)
      Proline residue:  C 100  - end of helix
    Processing helix  chain 'C' and resid 108 through 116
    Processing helix  chain 'C' and resid 121 through 142
    Processing helix  chain 'C' and resid 142 through 152
      removed outlier: 4.148A  pdb=" N   LEU C 146 " --> pdb=" O   ARG C 142 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR C 151 " --> pdb=" O   ALA C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 161 through 179
      Proline residue:  C 167  - end of helix
    Processing helix  chain 'C' and resid 185 through 199
      removed outlier: 4.117A  pdb=" N   GLN C 191 " --> pdb=" O   ALA C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 231
      removed outlier: 3.533A  pdb=" N   LEU C 224 " --> pdb=" O   PRO C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 255 through 259
    Processing helix  chain 'C' and resid 278 through 283
    Processing helix  chain 'C' and resid 297 through 304
    Processing helix  chain 'C' and resid 304 through 315
      removed outlier: 3.545A  pdb=" N   ASP C 309 " --> pdb=" O   LYS C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 333 through 345
      removed outlier: 3.652A  pdb=" N   LEU C 345 " --> pdb=" O   ASP C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 354 through 360
    Processing helix  chain 'C' and resid 381 through 400
    Processing helix  chain 'C' and resid 404 through 406
      No H-bonds generated for 'chain 'C' and resid 404 through 406'
    Processing helix  chain 'C' and resid 418 through 428
    Processing helix  chain 'C' and resid 447 through 459
    Processing helix  chain 'C' and resid 466 through 475
    Processing helix  chain 'C' and resid 476 through 483
    Processing helix  chain 'C' and resid 486 through 500
      removed outlier: 3.800A  pdb=" N   ARG C 491 " --> pdb=" O   GLU C 487 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   TYR C 492 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 507 through 514
    Processing helix  chain 'C' and resid 523 through 537
    Processing helix  chain 'C' and resid 558 through 578
      removed outlier: 3.971A  pdb=" N   GLY C 562 " --> pdb=" O   ALA C 558 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 583 through 588
    Processing helix  chain 'C' and resid 589 through 599
    Processing helix  chain 'C' and resid 605 through 626
    Processing helix  chain 'C' and resid 633 through 646
      removed outlier: 4.278A  pdb=" N   LEU C 637 " --> pdb=" O   PRO C 633 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASP C 646 " --> pdb=" O   ALA C 642 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 707 through 722
      removed outlier: 3.655A  pdb=" N   LEU C 717 " --> pdb=" O   ARG C 713 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 745 through 757
    Processing helix  chain 'C' and resid 768 through 780
    Processing helix  chain 'C' and resid 834 through 843
      removed outlier: 4.143A  pdb=" N   HIS C 843 " --> pdb=" O   ARG C 839 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 843 through 851
      removed outlier: 4.047A  pdb=" N   PHE C 849 " --> pdb=" O   VAL C 845 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   MET C 851 " --> pdb=" O   ALA C 847 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 874 through 889
      removed outlier: 3.704A  pdb=" N   ALA C 887 " --> pdb=" O   GLN C 883 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 894 through 904
    Processing helix  chain 'C' and resid 911 through 933
      removed outlier: 4.257A  pdb=" N   GLN C 926 " --> pdb=" O   GLN C 922 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   LEU C 927 " --> pdb=" O   GLU C 923 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ARG C 930 " --> pdb=" O   GLN C 926 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL C 931 " --> pdb=" O   LEU C 927 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 973 through 990
      removed outlier: 3.780A  pdb=" N   LEU C 980 " --> pdb=" O   GLN C 976 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER C 990 " --> pdb=" O   VAL C 986 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1001 through 1003
      No H-bonds generated for 'chain 'C' and resid 1001 through 1003'
    Processing helix  chain 'C' and resid 1012 through 1033
      removed outlier: 3.545A  pdb=" N   SER C1032 " --> pdb=" O   ARG C1028 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1040 through 1049
      removed outlier: 4.093A  pdb=" N   THR C1048 " --> pdb=" O   ALA C1044 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   CYS C1049 " --> pdb=" O   TRP C1045 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1062 through 1076
      removed outlier: 3.982A  pdb=" N   LYS C1066 " --> pdb=" O   SER C1062 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ARG C1068 " --> pdb=" O   LEU C1064 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1087 through 1094
      removed outlier: 4.032A  pdb=" N   LEU C1093 " --> pdb=" O   TRP C1089 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TRP C1094 " --> pdb=" O   TYR C1090 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1098 through 1113
    Processing helix  chain 'C' and resid 1114 through 1120
      removed outlier: 3.731A  pdb=" N   ARG C1118 " --> pdb=" O   LEU C1114 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE C1119 " --> pdb=" O   PRO C1115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 13
    Processing helix  chain 'D' and resid 17 through 29
    Processing helix  chain 'D' and resid 32 through 49
    Processing helix  chain 'D' and resid 54 through 62
      removed outlier: 3.652A  pdb=" N   LEU D  58 " --> pdb=" O   PRO D  54 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLU D  62 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 72
    Processing helix  chain 'D' and resid 80 through 87
    Processing helix  chain 'D' and resid 110 through 124
    Processing sheet with id=AA1, first strand: chain 'B' and resid 126 through 127
      removed outlier: 6.516A  pdb=" N   VAL B  61 " --> pdb=" O   PHE B 127 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   ILE B 383 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ARG B  19 " --> pdb=" O   LEU B 411 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   GLY B 413 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   ILE B  21 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TYR B 441 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152
      removed outlier: 6.526A  pdb=" N   GLN B 151 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 209
      removed outlier: 6.188A  pdb=" N   VAL B 207 " --> pdb=" O   LEU B 778 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR B 768 " --> pdb=" O   VAL B 777 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 489
      removed outlier: 3.583A  pdb=" N   MET B 541 " --> pdb=" O   ARG B 488 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580
      removed outlier: 6.058A  pdb=" N   VAL B 556 " --> pdb=" O   VAL B 739 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   CYS B 813 " --> pdb=" O   PRO B 750 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 752 " --> pdb=" O   CYS B 813 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 35 through 36
      removed outlier: 7.688A  pdb=" N   VAL C 211 " --> pdb=" O   HIS C 237 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   LEU C 239 " --> pdb=" O   VAL C 211 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   ILE C 213 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ARG C   3 " --> pdb=" O   LEU C 238 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 264 through 265
    Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366
      removed outlier: 7.199A  pdb=" N   ARG C 365 " --> pdb=" O   TYR C 760 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439
      removed outlier: 4.011A  pdb=" N   ASN C 660 " --> pdb=" O   ILE C 408 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   CYS C 662 " --> pdb=" O   VAL C 410 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LYS C 673 " --> pdb=" O   GLN C 724 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL C 675 " --> pdb=" O   LYS C 726 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER C 730 " --> pdb=" O   LEU C 677 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE C 729 " --> pdb=" O   THR C 375 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TYR C 731 " --> pdb=" O   HIS C 377 " (cutoff:3.500A)
      removed outlier: 8.684A  pdb=" N   CYS C 782 " --> pdb=" O   ILE C 374 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   PHE C 376 " --> pdb=" O   CYS C 782 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 831 through 833
      removed outlier: 6.198A  pdb=" N   VAL C 832 " --> pdb=" O   THR C 953 " (cutoff:3.500A)
      removed outlier: 8.733A  pdb=" N   TRP C 955 " --> pdb=" O   VAL C 832 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   GLN C 939 " --> pdb=" O   GLN C 958 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 965 through 967
      removed outlier: 6.787A  pdb=" N   ARG C 966 " --> pdb=" O   PHE C 999 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU C 998 " --> pdb=" O   TRP C1006 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 1050 through 1051
      removed outlier: 3.877A  pdb=" N   ASP C1051 " --> pdb=" O   ALA C1056 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ALA C1056 " --> pdb=" O   ASP C1051 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 92
      removed outlier: 3.809A  pdb=" N   LEU D 102 " --> pdb=" O   SER D  92 " (cutoff:3.500A)

    735 hydrogen bonds defined for protein.
    2163 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: 5.58

  Time building geometry restraints manager: 6.76 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: 5573
        1.34 -     1.46: 3311
        1.46 -     1.58: 8023
        1.58 -     1.70: 0
        1.70 -     1.82: 132
  Bond restraints: 17039
  Sorted by residual:
  bond pdb=" CA  ASN D  80 "
       pdb=" CB  ASN D  80 "
    ideal  model  delta    sigma   weight residual
    1.524  1.547 -0.023 1.37e-02 5.33e+03 2.85e+00
  bond pdb=" CG1 ILE B 865 "
       pdb=" CD1 ILE B 865 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.41e+00
  bond pdb=" CB  LYS B 268 "
       pdb=" CG  LYS B 268 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.01e+00
  bond pdb=" C   SER C 419 "
       pdb=" N   PRO C 420 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.017 1.36e-02 5.41e+03 1.62e+00
  bond pdb=" CA  ASN D  80 "
       pdb=" C   ASN D  80 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.016 1.35e-02 5.49e+03 1.48e+00
  ... (remaining 17034 not shown)

  Histogram of bond angle deviations from ideal:
       99.02 -   106.09: 449
      106.09 -   113.17: 8971
      113.17 -   120.25: 6512
      120.25 -   127.32: 6978
      127.32 -   134.40: 213
  Bond angle restraints: 23123
  Sorted by residual:
  angle pdb=" C   ASN D  80 "
        pdb=" CA  ASN D  80 "
        pdb=" CB  ASN D  80 "
      ideal   model   delta    sigma   weight residual
     111.41  119.87   -8.46 1.65e+00 3.67e-01 2.63e+01
  angle pdb=" C   PHE C 483 "
        pdb=" N   ASP C 484 "
        pdb=" CA  ASP C 484 "
      ideal   model   delta    sigma   weight residual
     121.54  130.24   -8.70 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" CB  MET B 499 "
        pdb=" CG  MET B 499 "
        pdb=" SD  MET B 499 "
      ideal   model   delta    sigma   weight residual
     112.70  124.71  -12.01 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" CB  LYS B 268 "
        pdb=" CG  LYS B 268 "
        pdb=" CD  LYS B 268 "
      ideal   model   delta    sigma   weight residual
     111.30  120.22   -8.92 2.30e+00 1.89e-01 1.50e+01
  angle pdb=" N   MET C 569 "
        pdb=" CA  MET C 569 "
        pdb=" CB  MET C 569 "
      ideal   model   delta    sigma   weight residual
     110.28  115.90   -5.62 1.55e+00 4.16e-01 1.32e+01
  ... (remaining 23118 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 9139
       17.44 -    34.89: 965
       34.89 -    52.33: 152
       52.33 -    69.78: 40
       69.78 -    87.22: 26
  Dihedral angle restraints: 10322
    sinusoidal: 4262
      harmonic: 6060
  Sorted by residual:
  dihedral pdb=" CA  LEU C 460 "
           pdb=" C   LEU C 460 "
           pdb=" N   PRO C 461 "
           pdb=" CA  PRO C 461 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.71  -23.29     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  SER C 268 "
           pdb=" C   SER C 268 "
           pdb=" N   PHE C 269 "
           pdb=" CA  PHE C 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.27  -22.73     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  ASP B 862 "
           pdb=" C   ASP B 862 "
           pdb=" N   ASP B 863 "
           pdb=" CA  ASP B 863 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.65   22.35     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 10319 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 2237
       0.073 -    0.146: 284
       0.146 -    0.218: 11
       0.218 -    0.291: 1
       0.291 -    0.364: 1
  Chirality restraints: 2534
  Sorted by residual:
  chirality pdb=" CB  ILE B 865 "
            pdb=" CA  ILE B 865 "
            pdb=" CG1 ILE B 865 "
            pdb=" CG2 ILE B 865 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" CB  THR C 402 "
            pdb=" CA  THR C 402 "
            pdb=" OG1 THR C 402 "
            pdb=" CG2 THR C 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  ASP C 484 "
            pdb=" N   ASP C 484 "
            pdb=" C   ASP C 484 "
            pdb=" CB  ASP C 484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 2531 not shown)

  Planarity restraints: 3042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C1114 "    0.055 5.00e-02 4.00e+02   8.30e-02 1.10e+01
        pdb=" N   PRO C1115 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO C1115 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO C1115 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 582 "    0.054 5.00e-02 4.00e+02   8.17e-02 1.07e+01
        pdb=" N   PRO C 583 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO C 583 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C 583 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 657 "   -0.049 5.00e-02 4.00e+02   7.40e-02 8.76e+00
        pdb=" N   PRO C 658 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO C 658 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 658 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 3039 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3687
        2.79 -     3.31: 15624
        3.31 -     3.84: 27053
        3.84 -     4.37: 29040
        4.37 -     4.90: 49456
  Nonbonded interactions: 124860
  Sorted by model distance:
  nonbonded pdb=" O   ARG C 112 "
            pdb=" OG1 THR C 116 "
     model   vdw
     2.257 2.440
  nonbonded pdb=" OH  TYR B 200 "
            pdb=" OE1 GLN B 765 "
     model   vdw
     2.290 2.440
  nonbonded pdb=" O   VAL B 804 "
            pdb=" NH2 ARG B 808 "
     model   vdw
     2.310 2.520
  nonbonded pdb=" O   SER B 720 "
            pdb=" OG  SER B 720 "
     model   vdw
     2.318 2.440
  nonbonded pdb=" OE2 GLU C 357 "
            pdb=" ND2 ASN C 363 "
     model   vdw
     2.322 2.520
  ... (remaining 124855 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  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:          4.730
  Check model and map are aligned:         0.270
  Set scattering table:                    0.150
  Process input model:                     41.000
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.060
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
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   0.061  17039  Z= 0.208
  Angle     :  0.752  12.011  23123  Z= 0.381
  Chirality :  0.046   0.364   2534
  Planarity :  0.006   0.083   3042
  Dihedral  : 14.956  87.219   6382
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -1.32 (0.18), residues: 2065
  helix: -0.12 (0.15), residues: 1037
  sheet: -1.37 (0.42), residues: 161
  loop : -1.63 (0.21), residues: 867

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.855 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2400
  time to fit residues: 34.9217
Evaluate side-chains
  72 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.939 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.5981
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 173 optimal weight:    9.9990
   chunk 156 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 105 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 161 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   chunk 120 optimal weight:    0.9980
   chunk 187 optimal weight:    4.9990
   overall best weight:    3.7386

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

Flipped N/Q/H residues before XYZ refinement:
B  79 ASN
B 181 GLN
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.032  17039  Z= 0.277
  Angle     :  0.591   7.320  23123  Z= 0.305
  Chirality :  0.040   0.162   2534
  Planarity :  0.005   0.072   3042
  Dihedral  :  4.667  21.612   2280
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.67 (0.19), residues: 2065
  helix:  0.63 (0.16), residues: 1039
  sheet: -1.73 (0.40), residues: 159
  loop : -1.48 (0.21), residues: 867

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2485
  time to fit residues: 34.1139
Evaluate side-chains
  68 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 2.088 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.7901
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 155 optimal weight:    1.9990
   chunk 127 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 187 optimal weight:    8.9990
   chunk 202 optimal weight:   10.0000
   chunk 166 optimal weight:    0.9990
   chunk 185 optimal weight:   20.0000
   chunk 63 optimal weight:    0.9990
   chunk 150 optimal weight:    0.9980
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  79 ASN
** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 714 HIS
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 817 HIS
** C 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.031  17039  Z= 0.158
  Angle     :  0.508   5.958  23123  Z= 0.260
  Chirality :  0.039   0.147   2534
  Planarity :  0.004   0.079   3042
  Dihedral  :  4.407  20.706   2280
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.23 (0.19), residues: 2065
  helix:  1.00 (0.16), residues: 1030
  sheet: -1.59 (0.40), residues: 157
  loop : -1.25 (0.22), residues: 878

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 2.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.2417
  time to fit residues: 35.9876
Evaluate side-chains
  69 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.800 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.4367
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 185 optimal weight:   20.0000
   chunk 140 optimal weight:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0020
   chunk 89 optimal weight:    1.9990
   chunk 125 optimal weight:   10.0000
   chunk 188 optimal weight:    6.9990
   chunk 199 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 178 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0670
   overall best weight:    2.2132

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

Flipped N/Q/H residues before XYZ refinement:
B  79 ASN
B 224 GLN
** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 714 HIS
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.024  17039  Z= 0.182
  Angle     :  0.512   6.157  23123  Z= 0.261
  Chirality :  0.039   0.157   2534
  Planarity :  0.004   0.077   3042
  Dihedral  :  4.311  21.949   2280
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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 (0.19), residues: 2065
  helix:  1.08 (0.16), residues: 1042
  sheet: -1.36 (0.41), residues: 153
  loop : -1.27 (0.22), residues: 870

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.855 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2578
  time to fit residues: 37.3623
Evaluate side-chains
  68 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 2.076 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.7577
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 165 optimal weight:    9.9990
   chunk 113 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 148 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 169 optimal weight:    6.9990
   chunk 137 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 101 optimal weight:    5.9990
   chunk 178 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 278 ASN
B 714 HIS
B 737 GLN
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027  17039  Z= 0.170
  Angle     :  0.511   7.050  23123  Z= 0.259
  Chirality :  0.039   0.153   2534
  Planarity :  0.004   0.079   3042
  Dihedral  :  4.231  21.584   2280
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.01 (0.19), residues: 2065
  helix:  1.18 (0.16), residues: 1043
  sheet: -1.36 (0.41), residues: 153
  loop : -1.22 (0.22), residues: 869

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2589
  time to fit residues: 37.5512
Evaluate side-chains
  68 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 1.981 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.6572
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 179 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 116 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 199 optimal weight:   10.0000
   chunk 165 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 104 optimal weight:    7.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 150 GLN
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 673 ASN
B 714 HIS
C 233 HIS
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 615 GLN
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.037  17039  Z= 0.373
  Angle     :  0.681   8.650  23123  Z= 0.344
  Chirality :  0.043   0.157   2534
  Planarity :  0.005   0.078   3042
  Dihedral  :  4.724  21.653   2280
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.50 (0.19), residues: 2065
  helix:  0.75 (0.16), residues: 1039
  sheet: -1.57 (0.41), residues: 152
  loop : -1.39 (0.22), residues: 874

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2642
  time to fit residues: 35.8062
Evaluate side-chains
  67 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.795 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.4734
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 192 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 113 optimal weight:    4.9990
   chunk 145 optimal weight:    0.0870
   chunk 112 optimal weight:    5.9990
   chunk 167 optimal weight:    0.8980
   chunk 111 optimal weight:    9.9990
   chunk 198 optimal weight:   10.0000
   chunk 124 optimal weight:    1.9990
   chunk 121 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   overall best weight:    1.7562

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

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
B 673 ASN
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 822 GLN
** D  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.032  17039  Z= 0.164
  Angle     :  0.530   7.638  23123  Z= 0.268
  Chirality :  0.040   0.150   2534
  Planarity :  0.004   0.077   3042
  Dihedral  :  4.380  20.601   2280
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.08 (0.19), residues: 2065
  helix:  1.12 (0.16), residues: 1035
  sheet: -1.46 (0.41), residues: 153
  loop : -1.21 (0.22), residues: 877

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.2594
  time to fit residues: 38.8171
Evaluate side-chains
  69 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 2.003 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.7062
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 122 optimal weight:    9.9990
   chunk 79 optimal weight:    7.9990
   chunk 118 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 126 optimal weight:    4.9990
   chunk 135 optimal weight:    6.9990
   chunk 98 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 156 optimal weight:    9.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 673 ASN
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 920 GLN
** D  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.036  17039  Z= 0.259
  Angle     :  0.590   8.899  23123  Z= 0.296
  Chirality :  0.041   0.160   2534
  Planarity :  0.004   0.076   3042
  Dihedral  :  4.466  20.890   2280
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.23 (0.19), residues: 2065
  helix:  0.98 (0.16), residues: 1055
  sheet: -1.43 (0.41), residues: 152
  loop : -1.34 (0.22), residues: 858

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2624
  time to fit residues: 36.3454
Evaluate side-chains
  68 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 2.106 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.8576
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 180 optimal weight:    3.9990
   chunk 190 optimal weight:    5.9990
   chunk 173 optimal weight:    5.9990
   chunk 185 optimal weight:   10.0000
   chunk 111 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 145 optimal weight:   20.0000
   chunk 56 optimal weight:    9.9990
   chunk 167 optimal weight:    5.9990
   chunk 174 optimal weight:    0.9990
   chunk 184 optimal weight:    5.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 673 ASN
C 233 HIS
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035  17039  Z= 0.227
  Angle     :  0.570   8.188  23123  Z= 0.286
  Chirality :  0.040   0.153   2534
  Planarity :  0.004   0.076   3042
  Dihedral  :  4.438  20.736   2280
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer Outliers :  0.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.15 (0.19), residues: 2065
  helix:  1.04 (0.16), residues: 1054
  sheet: -1.41 (0.42), residues: 152
  loop : -1.28 (0.22), residues: 859

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 1.947 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2642
  time to fit residues: 38.2511
Evaluate side-chains
  68 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 1.924 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.7295
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 121 optimal weight:    6.9990
   chunk 195 optimal weight:    9.9990
   chunk 119 optimal weight:    4.9990
   chunk 92 optimal weight:    7.9990
   chunk 136 optimal weight:    8.9990
   chunk 205 optimal weight:   10.0000
   chunk 188 optimal weight:    9.9990
   chunk 163 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 126 optimal weight:    4.9990
   chunk 100 optimal weight:    9.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 673 ASN
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.038  17039  Z= 0.358
  Angle     :  0.684   8.880  23123  Z= 0.345
  Chirality :  0.043   0.158   2534
  Planarity :  0.005   0.074   3042
  Dihedral  :  4.824  23.745   2280
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.48 (0.19), residues: 2065
  helix:  0.77 (0.16), residues: 1040
  sheet: -1.53 (0.41), residues: 151
  loop : -1.41 (0.22), residues: 874

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

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

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4130 Ramachandran restraints generated.
    2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 2.025 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2978
  time to fit residues: 39.4811
Evaluate side-chains
  64 residues out of total 1784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.906 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.6020
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 129 optimal weight:    8.9990
   chunk 174 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   chunk 150 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0870
   chunk 163 optimal weight:    7.9990
   chunk 68 optimal weight:    0.3980
   chunk 168 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    1.0962

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 673 ASN
** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 297 ASN
** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.049674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.039091 restraints weight = 128465.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.040118 restraints weight = 77355.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.040787 restraints weight = 54994.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.032  17039  Z= 0.146
  Angle     :  0.544   8.769  23123  Z= 0.271
  Chirality :  0.040   0.154   2534
  Planarity :  0.004   0.076   3042
  Dihedral  :  4.370  21.972   2280
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer Outliers :  0.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.96 %
    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: -0.01 (0.19), residues: 2065
  helix:  1.19 (0.16), residues: 1036
  sheet: -1.36 (0.42), residues: 153
  loop : -1.21 (0.22), residues: 876

===============================================================================
Job complete
usr+sys time: 2178.69 seconds
wall clock time: 41 minutes 26.84 seconds (2486.84 seconds total)