Starting phenix.real_space_refine
on Thu Mar  5 04:53:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mr0_23952/03_2026/7mr0_23952.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mr0_23952/03_2026/7mr0_23952.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mr0_23952/03_2026/7mr0_23952.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mr0_23952/03_2026/7mr0_23952.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mr0_23952/03_2026/7mr0_23952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mr0_23952/03_2026/7mr0_23952.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      89      5.16       5
     C   12214      2.51       5
     N    3378      2.21       5
     O    3601      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19282
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 9247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1156, 9247
          Classifications: {'peptide': 1156}
          Link IDs: {'PTRANS': 52, 'TRANS': 1103}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 9078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1121, 9078
          Classifications: {'peptide': 1121}
          Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053}
    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: 4.31, per 1000 atoms: 0.22
  Number of scatterers: 19282
  At special positions: 0
  Unit cell: (150.29, 127.69, 141.25, 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      89     16.00
     O    3601      8.00
     N    3378      7.00
     C   12214      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.50
  Conformation dependent library (CDL) restraints added in 862.9 milliseconds
  

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4544

  Finding SS restraints...
    Secondary structure from input PDB file:
      111 helices and 17 sheets defined
      56.0% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 43
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.612A  pdb=" N   ALA B  49 " --> pdb=" O   GLY B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 59
      removed outlier: 3.640A  pdb=" N   GLU B  58 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU B  59 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 55 through 59'
    Processing helix  chain 'B' and resid 65 through 90
    Processing helix  chain 'B' and resid 94 through 104
    Processing helix  chain 'B' and resid 106 through 121
    Processing helix  chain 'B' and resid 122 through 124
      No H-bonds generated for 'chain 'B' and resid 122 through 124'
    Processing helix  chain 'B' and resid 128 through 140
      removed outlier: 3.715A  pdb=" N   ARG B 135 " --> pdb=" O   GLY B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 145
    Processing helix  chain 'B' and resid 156 through 172
    Processing helix  chain 'B' and resid 176 through 187
      removed outlier: 4.188A  pdb=" N   VAL B 182 " --> pdb=" O   GLU B 178 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   GLU B 185 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   THR B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 202
      removed outlier: 5.702A  pdb=" N   ARG B 199 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   TYR B 200 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   GLN B 202 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 240
      removed outlier: 3.979A  pdb=" N   VAL B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 266
    Processing helix  chain 'B' and resid 275 through 281
      removed outlier: 3.914A  pdb=" N   ASN B 278 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER B 279 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   TYR B 280 " --> pdb=" O   THR B 277 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLN B 281 " --> pdb=" O   ASN B 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 275 through 281'
    Processing helix  chain 'B' and resid 282 through 288
    Processing helix  chain 'B' and resid 308 through 318
      removed outlier: 3.970A  pdb=" N   ASP B 314 " --> pdb=" O   PHE B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 347
      removed outlier: 4.352A  pdb=" N   ARG B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   GLU B 337 " --> pdb=" O   ALA B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 364
    Processing helix  chain 'B' and resid 366 through 378
      removed outlier: 3.887A  pdb=" N   LEU B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 402
    Processing helix  chain 'B' and resid 414 through 418
      removed outlier: 3.524A  pdb=" N   GLN B 417 " --> pdb=" O   ASP B 414 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ALA B 418 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 414 through 418'
    Processing helix  chain 'B' and resid 427 through 437
    Processing helix  chain 'B' and resid 450 through 462
      removed outlier: 3.664A  pdb=" N   ASN B 455 " --> pdb=" O   PRO B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 534
    Processing helix  chain 'B' and resid 560 through 574
    Processing helix  chain 'B' and resid 586 through 589
      removed outlier: 3.920A  pdb=" N   GLU B 589 " --> pdb=" O   SER B 586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 586 through 589'
    Processing helix  chain 'B' and resid 590 through 605
      removed outlier: 4.294A  pdb=" N   GLN B 594 " --> pdb=" O   THR B 590 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   THR B 605 " --> pdb=" O   GLN B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 617
    Processing helix  chain 'B' and resid 624 through 634
      removed outlier: 3.714A  pdb=" N   ASP B 634 " --> pdb=" O   THR B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 656
    Processing helix  chain 'B' and resid 657 through 669
    Processing helix  chain 'B' and resid 669 through 677
    Processing helix  chain 'B' and resid 680 through 701
      removed outlier: 3.803A  pdb=" N   GLN B 700 " --> pdb=" O   GLU B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 704 through 717
    Processing helix  chain 'B' and resid 742 through 745
      removed outlier: 3.627A  pdb=" N   LYS B 745 " --> pdb=" O   HIS B 742 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 742 through 745'
    Processing helix  chain 'B' and resid 783 through 808
      removed outlier: 3.664A  pdb=" N   VAL B 787 " --> pdb=" O   ALA B 783 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 832 through 835
    Processing helix  chain 'B' and resid 836 through 843
      removed outlier: 3.669A  pdb=" N   LEU B 841 " --> pdb=" O   ALA B 837 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 849 through 860
      removed outlier: 3.846A  pdb=" N   LEU B 860 " --> pdb=" O   CYS B 856 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 916 through 921
    Processing helix  chain 'B' and resid 941 through 945
    Processing helix  chain 'B' and resid 949 through 959
      removed outlier: 4.184A  pdb=" N   PHE B 959 " --> pdb=" O   LEU B 955 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 969 through 980
    Processing helix  chain 'B' and resid 983 through 985
      No H-bonds generated for 'chain 'B' and resid 983 through 985'
    Processing helix  chain 'B' and resid 986 through 998
      removed outlier: 3.739A  pdb=" N   GLU B 992 " --> pdb=" O   PRO B 988 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   THR B 995 " --> pdb=" O   THR B 991 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1008 through 1012
    Processing helix  chain 'B' and resid 1013 through 1015
      No H-bonds generated for 'chain 'B' and resid 1013 through 1015'
    Processing helix  chain 'B' and resid 1032 through 1041
      removed outlier: 3.591A  pdb=" N   ASP B1037 " --> pdb=" O   ALA B1033 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   LEU B1039 " --> pdb=" O   GLN B1035 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1044 through 1049
      removed outlier: 4.188A  pdb=" N   GLY B1049 " --> pdb=" O   LEU B1046 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1089 through 1094
      removed outlier: 4.110A  pdb=" N   THR B1094 " --> pdb=" O   SER B1091 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1096 through 1106
    Processing helix  chain 'B' and resid 1107 through 1126
      removed outlier: 4.069A  pdb=" N   TYR B1111 " --> pdb=" O   TYR B1107 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLN B1112 " --> pdb=" O   ASP B1108 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   HIS B1124 " --> pdb=" O   ARG B1120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1130 through 1135
    Processing helix  chain 'B' and resid 1163 through 1173
      removed outlier: 3.812A  pdb=" N   GLU B1170 " --> pdb=" O   ALA B1166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 24
      removed outlier: 4.216A  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: 3.711A  pdb=" N   THR C  97 " --> pdb=" O   TRP C  93 " (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 143 through 152
      removed outlier: 3.911A  pdb=" N   THR C 151 " --> pdb=" O   ALA C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 161 through 180
      Proline residue:  C 167  - end of helix
      removed outlier: 3.770A  pdb=" N   GLY C 180 " --> pdb=" O   THR C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 199
      removed outlier: 4.106A  pdb=" N   TYR C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   GLN C 191 " --> pdb=" O   ALA C 187 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ARG C 192 " --> pdb=" O   ASN C 188 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER C 199 " --> pdb=" O   GLU C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 231
    Processing helix  chain 'C' and resid 255 through 260
    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
    Processing helix  chain 'C' and resid 333 through 345
    Processing helix  chain 'C' and resid 354 through 360
    Processing helix  chain 'C' and resid 381 through 400
      removed outlier: 3.657A  pdb=" N   ASP C 391 " --> pdb=" O   GLU C 387 " (cutoff:3.500A)
    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 429
    Processing helix  chain 'C' and resid 430 through 434
      removed outlier: 3.744A  pdb=" N   TYR C 434 " --> pdb=" O   ALA C 431 " (cutoff:3.500A)
    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
      removed outlier: 4.053A  pdb=" N   PHE C 483 " --> pdb=" O   LEU C 479 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 486 through 501
      removed outlier: 4.378A  pdb=" N   TYR C 492 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLN C 495 " --> pdb=" O   ARG C 491 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLY C 501 " --> pdb=" O   VAL C 497 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 507 through 513
    Processing helix  chain 'C' and resid 523 through 537
    Processing helix  chain 'C' and resid 538 through 542
      removed outlier: 3.631A  pdb=" N   GLN C 541 " --> pdb=" O   GLU C 538 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   GLY C 542 " --> pdb=" O   SER C 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 538 through 542'
    Processing helix  chain 'C' and resid 557 through 578
      removed outlier: 4.309A  pdb=" N   VAL C 561 " --> pdb=" O   ILE C 557 " (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 604 through 626
      removed outlier: 4.330A  pdb=" N   ALA C 608 " --> pdb=" O   GLU C 604 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 633 through 645
      removed outlier: 3.922A  pdb=" N   LEU C 637 " --> pdb=" O   PRO C 633 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP C 639 " --> pdb=" O   SER C 635 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLN C 643 " --> pdb=" O   ASP C 639 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 707 through 722
      removed outlier: 3.597A  pdb=" N   LEU C 717 " --> pdb=" O   ARG C 713 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 745 through 758
    Processing helix  chain 'C' and resid 768 through 780
    Processing helix  chain 'C' and resid 790 through 795
      removed outlier: 4.071A  pdb=" N   TYR C 794 " --> pdb=" O   ASP C 790 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 806 through 811
    Processing helix  chain 'C' and resid 833 through 843
      removed outlier: 4.243A  pdb=" N   HIS C 843 " --> pdb=" O   ARG C 839 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 843 through 852
    Processing helix  chain 'C' and resid 873 through 889
    Processing helix  chain 'C' and resid 893 through 904
      removed outlier: 4.049A  pdb=" N   LEU C 897 " --> pdb=" O   ASP C 893 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 910 through 933
      removed outlier: 3.832A  pdb=" N   GLN C 926 " --> pdb=" O   GLN C 922 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG C 930 " --> pdb=" O   GLN C 926 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 973 through 990
    Processing helix  chain 'C' and resid 1012 through 1033
      removed outlier: 3.871A  pdb=" N   SER C1032 " --> pdb=" O   ARG C1028 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1038 through 1050
    Processing helix  chain 'C' and resid 1060 through 1076
    Processing helix  chain 'C' and resid 1087 through 1094
    Processing helix  chain 'C' and resid 1098 through 1113
    Processing helix  chain 'C' and resid 1113 through 1120
    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 48
    Processing helix  chain 'D' and resid 54 through 61
    Processing helix  chain 'D' and resid 66 through 72
    Processing helix  chain 'D' and resid 80 through 88
      removed outlier: 4.020A  pdb=" N   SER D  88 " --> pdb=" O   CYS D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 124
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7
      removed outlier: 5.775A  pdb=" N   GLU B   6 " --> pdb=" O   THR B 442 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU B 411 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 126 through 127
      removed outlier: 5.798A  pdb=" N   VAL B  61 " --> pdb=" O   PHE B 127 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   LEU B  60 " --> pdb=" O   MET B 382 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 152
      removed outlier: 6.779A  pdb=" N   GLN B 151 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 207 through 208
      removed outlier: 6.272A  pdb=" N   VAL B 207 " --> pdb=" O   LEU B 778 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   TYR B 768 " --> pdb=" O   VAL B 777 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 446
    Processing sheet with id=AA6, first strand: chain 'B' and resid 490 through 491
      removed outlier: 3.627A  pdb=" N   VAL B 490 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU B 539 " --> pdb=" O   VAL B 490 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 578 through 580
      removed outlier: 6.603A  pdb=" N   VAL B 579 " --> pdb=" O   ILE B 738 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   THR B 740 " --> pdb=" O   VAL B 579 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN B 737 " --> pdb=" O   ILE B 554 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TRP B 753 " --> pdb=" O   SER B 555 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL B 752 " --> pdb=" O   HIS B 812 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   SER B 814 " --> pdb=" O   VAL B 752 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 815 " --> pdb=" O   LYS B 500 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 901 through 904
      removed outlier: 3.658A  pdb=" N   MET B1061 " --> pdb=" O   ARG B 902 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   THR B 904 " --> pdb=" O   MET B1061 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   VAL B1058 " --> pdb=" O   GLU B1029 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   GLU B1029 " --> pdb=" O   VAL B1058 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1017 through 1022
      removed outlier: 7.209A  pdb=" N   ASP B1067 " --> pdb=" O   GLU B1020 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   GLU B1022 " --> pdb=" O   PHE B1065 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   PHE B1065 " --> pdb=" O   GLU B1022 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1079 through 1080
      removed outlier: 6.494A  pdb=" N   ASP B1080 " --> pdb=" O   LEU B1141 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 61
      removed outlier: 4.727A  pdb=" N   MET C  34 " --> pdb=" O   ARG C 210 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   VAL C 211 " --> pdb=" O   HIS C 237 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   LEU C 239 " --> pdb=" O   VAL C 211 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ILE C 213 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   THR C 241 " --> pdb=" O   ILE C 213 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER C   7 " --> pdb=" O   PHE C 240 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   LEU C   2 " --> pdb=" O   GLN C 321 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   LEU C 323 " --> pdb=" O   LEU C   2 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   VAL C   4 " --> pdb=" O   LEU C 323 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ARG C 265 " --> pdb=" O   ASP C 324 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLN C 264 " --> pdb=" O   ARG C 272 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 365 through 366
      removed outlier: 6.369A  pdb=" N   ARG C 365 " --> pdb=" O   TYR C 760 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 437 through 439
      removed outlier: 6.456A  pdb=" N   ALA C 438 " --> pdb=" O   ILE C 661 " (cutoff:3.500A)
      removed outlier: 8.689A  pdb=" N   THR C 663 " --> pdb=" O   ALA C 438 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU C 678 " --> pdb=" O   MET C 411 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   LYS C 673 " --> pdb=" O   GLN C 724 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   VAL C 675 " --> pdb=" O   LYS C 726 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   THR C 375 " --> pdb=" O   LEU C 727 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE C 729 " --> pdb=" O   THR C 375 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TYR C 731 " --> pdb=" O   HIS C 377 " (cutoff:3.500A)
      removed outlier: 9.066A  pdb=" N   CYS C 782 " --> pdb=" O   ILE C 374 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   PHE C 376 " --> pdb=" O   CYS C 782 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 442 through 443
      removed outlier: 4.243A  pdb=" N   ARG C 442 " --> pdb=" O   ILE C 650 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE C 650 " --> pdb=" O   ARG C 442 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'C' and resid 942 through 947
      removed outlier: 3.526A  pdb=" N   LEU C 945 " --> pdb=" O   ILE C 952 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 963 through 967
      removed outlier: 5.636A  pdb=" N   LEU C 964 " --> pdb=" O   ARG C 997 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   PHE C 999 " --> pdb=" O   LEU C 964 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG C 966 " --> pdb=" O   PHE C 999 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 102

    900 hydrogen bonds defined for protein.
    2655 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.61

  Time building geometry restraints manager: 1.99 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: 6534
        1.34 -     1.46: 4311
        1.46 -     1.58: 8730
        1.58 -     1.70: 1
        1.70 -     1.82: 149
  Bond restraints: 19725
  Sorted by residual:
  bond pdb=" C   CYS B1050 "
       pdb=" N   PRO B1051 "
    ideal  model  delta    sigma   weight residual
    1.329  1.385 -0.056 1.18e-02 7.18e+03 2.23e+01
  bond pdb=" CA  MET B 121 "
       pdb=" C   MET B 121 "
    ideal  model  delta    sigma   weight residual
    1.522  1.576 -0.054 1.41e-02 5.03e+03 1.46e+01
  bond pdb=" C   LEU C 460 "
       pdb=" N   PRO C 461 "
    ideal  model  delta    sigma   weight residual
    1.337  1.378 -0.042 1.11e-02 8.12e+03 1.40e+01
  bond pdb=" C   HIS C 448 "
       pdb=" N   PRO C 449 "
    ideal  model  delta    sigma   weight residual
    1.335  1.381 -0.046 1.30e-02 5.92e+03 1.23e+01
  bond pdb=" CA  CYS B1050 "
       pdb=" C   CYS B1050 "
    ideal  model  delta    sigma   weight residual
    1.523  1.545 -0.022 1.00e-02 1.00e+04 4.76e+00
  ... (remaining 19720 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 26301
        2.49 -     4.99: 387
        4.99 -     7.48: 77
        7.48 -     9.98: 16
        9.98 -    12.47: 3
  Bond angle restraints: 26784
  Sorted by residual:
  angle pdb=" N   GLY B1137 "
        pdb=" CA  GLY B1137 "
        pdb=" C   GLY B1137 "
      ideal   model   delta    sigma   weight residual
     110.97  119.40   -8.43 1.42e+00 4.96e-01 3.52e+01
  angle pdb=" CA  SER B 619 "
        pdb=" C   SER B 619 "
        pdb=" N   MET B 620 "
      ideal   model   delta    sigma   weight residual
     118.08  125.53   -7.45 1.30e+00 5.92e-01 3.28e+01
  angle pdb=" N   ILE B1139 "
        pdb=" CA  ILE B1139 "
        pdb=" C   ILE B1139 "
      ideal   model   delta    sigma   weight residual
     107.37  114.61   -7.24 1.48e+00 4.57e-01 2.39e+01
  angle pdb=" N   GLU B1054 "
        pdb=" CA  GLU B1054 "
        pdb=" C   GLU B1054 "
      ideal   model   delta    sigma   weight residual
     113.02  107.27    5.75 1.20e+00 6.94e-01 2.29e+01
  angle pdb=" C   ILE B 229 "
        pdb=" N   ASP B 230 "
        pdb=" CA  ASP B 230 "
      ideal   model   delta    sigma   weight residual
     121.58  112.95    8.63 1.95e+00 2.63e-01 1.96e+01
  ... (remaining 26779 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 10556
       17.99 -    35.98: 1078
       35.98 -    53.97: 219
       53.97 -    71.96: 35
       71.96 -    89.94: 24
  Dihedral angle restraints: 11912
    sinusoidal: 4906
      harmonic: 7006
  Sorted by residual:
  dihedral pdb=" CA  LEU B 581 "
           pdb=" C   LEU B 581 "
           pdb=" N   SER B 582 "
           pdb=" CA  SER B 582 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.32  -24.68     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  VAL C 889 "
           pdb=" C   VAL C 889 "
           pdb=" N   GLU C 890 "
           pdb=" CA  GLU C 890 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.83  -23.17     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  PRO B 405 "
           pdb=" C   PRO B 405 "
           pdb=" N   GLU B 406 "
           pdb=" CA  GLU B 406 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.41  -21.59     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 11909 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 2460
       0.063 -    0.126: 412
       0.126 -    0.189: 40
       0.189 -    0.252: 3
       0.252 -    0.315: 1
  Chirality restraints: 2916
  Sorted by residual:
  chirality pdb=" CB  THR B 605 "
            pdb=" CA  THR B 605 "
            pdb=" OG1 THR B 605 "
            pdb=" CG2 THR B 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.24    0.32 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CA  GLU C  79 "
            pdb=" N   GLU C  79 "
            pdb=" C   GLU C  79 "
            pdb=" CB  GLU C  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  ILE D  75 "
            pdb=" CA  ILE D  75 "
            pdb=" CG1 ILE D  75 "
            pdb=" CG2 ILE D  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.55e-01
  ... (remaining 2913 not shown)

  Planarity restraints: 3530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 253 "    0.081 5.00e-02 4.00e+02   1.22e-01 2.39e+01
        pdb=" N   PRO C 254 "   -0.211 5.00e-02 4.00e+02
        pdb=" CA  PRO C 254 "    0.067 5.00e-02 4.00e+02
        pdb=" CD  PRO C 254 "    0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 310 "    0.022 2.00e-02 2.50e+03   2.55e-02 1.13e+01
        pdb=" CG  PHE B 310 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 310 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 310 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 310 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 310 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 657 "    0.049 5.00e-02 4.00e+02   7.44e-02 8.85e+00
        pdb=" N   PRO C 658 "   -0.129 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 3527 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 4888
        2.81 -     3.33: 17346
        3.33 -     3.85: 29917
        3.85 -     4.38: 32042
        4.38 -     4.90: 56878
  Nonbonded interactions: 141071
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 276 "
            pdb=" OG  SER C 280 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   SER B 462 "
            pdb=" OG  SER B 462 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   ALA D  90 "
            pdb=" OG1 THR D  98 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER B1090 "
            pdb=" OE1 GLN B1153 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OH  TYR B 161 "
            pdb=" OE1 GLN B 191 "
     model   vdw
     2.319 3.040
  ... (remaining 141066 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
========== 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:             1.530
  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:             0.030
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.000
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
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   0.079  19725  Z= 0.183
  Angle     :  0.810  12.471  26784  Z= 0.443
  Chirality :  0.047   0.315   2916
  Planarity :  0.006   0.122   3530
  Dihedral  : 15.125  89.944   7368
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  5.77 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  0.53 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.16), residues: 2392
  helix: -0.16 (0.14), residues: 1207
  sheet: -1.60 (0.38), residues: 189
  loop : -2.45 (0.18), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 135 
 TYR   0.025   0.001   TYR C 190 
 PHE   0.059   0.001   PHE B 310 
 TRP   0.028   0.001   TRP B1085 
 HIS   0.008   0.001   HIS B 689 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (19725)
  covalent geometry    : angle       0.81050 (26784)
  hydrogen bonds       : bond        0.12839 (  900)
  hydrogen bonds       : angle       5.27755 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
REVERT: B  518 MET cc_start: 0.8038 (mmm) cc_final: 0.7370 (mmm)
  outliers start: 9
  outliers final: 2
  residues processed: 162
  average time/residue: 0.1158
  time to fit residues: 31.7778
Evaluate side-chains
  121 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1047 SER
Chi-restraints excluded: chain B residue 1138 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 216 optimal weight:    7.9990
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    3.9990
   chunk 227 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0980
   chunk 235 optimal weight:   20.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
B 714 HIS
B 742 HIS
B 943 HIS
B 944 GLN
C 757 GLN
C 850 GLN
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  15 GLN
D  80 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.107728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.085120 restraints weight = 52809.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.085241 restraints weight = 31076.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.086165 restraints weight = 22713.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086555 restraints weight = 19170.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.086750 restraints weight = 17386.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.0918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  19725  Z= 0.113
  Angle     :  0.553   8.274  26784  Z= 0.281
  Chirality :  0.040   0.173   2916
  Planarity :  0.005   0.075   3530
  Dihedral  :  4.493  22.699   2643
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  7.09 %
    Favored  : 92.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.17), residues: 2392
  helix:  0.72 (0.15), residues: 1216
  sheet: -1.68 (0.36), residues: 200
  loop : -2.28 (0.18), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 728 
 TYR   0.020   0.001   TYR C1075 
 PHE   0.019   0.001   PHE B 127 
 TRP   0.013   0.001   TRP C 574 
 HIS   0.008   0.001   HIS C1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (19725)
  covalent geometry    : angle       0.55301 (26784)
  hydrogen bonds       : bond        0.04053 (  900)
  hydrogen bonds       : angle       4.43132 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 MET cc_start: 0.8038 (mmt) cc_final: 0.7808 (mmt)
REVERT: B  453 MET cc_start: 0.8420 (mmm) cc_final: 0.8124 (tpt)
REVERT: B  518 MET cc_start: 0.8328 (mmm) cc_final: 0.8016 (mmm)
REVERT: B  621 MET cc_start: 0.9009 (mmm) cc_final: 0.8690 (tpp)
REVERT: C   96 MET cc_start: 0.8707 (tpp) cc_final: 0.8330 (ttm)
REVERT: C 1031 MET cc_start: 0.8989 (tpp) cc_final: 0.8070 (mpp)
  outliers start: 8
  outliers final: 4
  residues processed: 130
  average time/residue: 0.1084
  time to fit residues: 24.0956
Evaluate side-chains
  120 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain C residue  953 THR
Chi-restraints excluded: chain D residue   53 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 195 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 147 optimal weight:    1.9990
   chunk 167 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 144 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 109 optimal weight:    5.9990
   chunk 186 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   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  81 HIS
B 222 HIS
B 404 GLN
B 610 ASN
B 910 GLN
B 911 GLN
C 228 GLN
C 510 ASN
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.104917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.082407 restraints weight = 52693.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.082482 restraints weight = 35321.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.082953 restraints weight = 29027.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.083233 restraints weight = 23870.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.083416 restraints weight = 20868.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  19725  Z= 0.225
  Angle     :  0.670  14.370  26784  Z= 0.340
  Chirality :  0.043   0.143   2916
  Planarity :  0.005   0.066   3530
  Dihedral  :  4.909  25.525   2641
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  9.91 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.17), residues: 2392
  helix:  0.69 (0.15), residues: 1220
  sheet: -1.68 (0.37), residues: 195
  loop : -2.28 (0.19), residues: 977

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 135 
 TYR   0.021   0.002   TYR C 728 
 PHE   0.032   0.002   PHE B 127 
 TRP   0.018   0.002   TRP B 901 
 HIS   0.008   0.002   HIS C 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (19725)
  covalent geometry    : angle       0.67004 (26784)
  hydrogen bonds       : bond        0.06065 (  900)
  hydrogen bonds       : angle       4.78125 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  187 TRP cc_start: 0.7159 (OUTLIER) cc_final: 0.6329 (p90)
REVERT: B  518 MET cc_start: 0.8533 (mmm) cc_final: 0.8302 (mmm)
REVERT: B  727 MET cc_start: 0.6232 (mtt) cc_final: 0.5921 (mtt)
REVERT: C   96 MET cc_start: 0.8670 (tpp) cc_final: 0.8310 (ttm)
REVERT: C  446 GLN cc_start: 0.7946 (tp40) cc_final: 0.7360 (tp-100)
REVERT: C 1031 MET cc_start: 0.9309 (tpp) cc_final: 0.8641 (tpp)
  outliers start: 24
  outliers final: 14
  residues processed: 135
  average time/residue: 0.1062
  time to fit residues: 24.4132
Evaluate side-chains
  129 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 TRP
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  699 THR
Chi-restraints excluded: chain B residue  809 SER
Chi-restraints excluded: chain B residue  888 LEU
Chi-restraints excluded: chain B residue 1138 VAL
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain D residue   26 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 199 optimal weight:    7.9990
   chunk 142 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 228 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 195 optimal weight:    5.9990
   chunk 96 optimal weight:    8.9990
   chunk 224 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
B 910 GLN
** C 960 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 = 0.3890 r_free = 0.3890 target = 0.106678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.085044 restraints weight = 53565.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.084475 restraints weight = 35570.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.085219 restraints weight = 28959.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.085615 restraints weight = 22283.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.085808 restraints weight = 20374.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  19725  Z= 0.119
  Angle     :  0.553  10.670  26784  Z= 0.278
  Chirality :  0.040   0.143   2916
  Planarity :  0.004   0.060   3530
  Dihedral  :  4.572  24.220   2641
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.75 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.17), residues: 2392
  helix:  1.05 (0.15), residues: 1217
  sheet: -1.83 (0.35), residues: 207
  loop : -2.17 (0.19), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 135 
 TYR   0.012   0.001   TYR B 394 
 PHE   0.016   0.001   PHE B 127 
 TRP   0.013   0.001   TRP C 616 
 HIS   0.007   0.001   HIS C1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (19725)
  covalent geometry    : angle       0.55348 (26784)
  hydrogen bonds       : bond        0.04372 (  900)
  hydrogen bonds       : angle       4.43394 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 MET cc_start: 0.8207 (mmt) cc_final: 0.7989 (mmt)
REVERT: B  187 TRP cc_start: 0.7104 (OUTLIER) cc_final: 0.6385 (p90)
REVERT: B  518 MET cc_start: 0.8272 (mmm) cc_final: 0.8008 (mmm)
REVERT: B  727 MET cc_start: 0.6384 (mtt) cc_final: 0.6088 (mtt)
REVERT: C   96 MET cc_start: 0.8732 (tpp) cc_final: 0.8406 (ttm)
REVERT: C  452 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7526 (mp0)
REVERT: C  978 MET cc_start: 0.8900 (tmm) cc_final: 0.8378 (tmm)
REVERT: C 1031 MET cc_start: 0.9239 (tpp) cc_final: 0.8361 (tpp)
REVERT: D  118 THR cc_start: 0.6070 (p) cc_final: 0.5797 (t)
  outliers start: 24
  outliers final: 15
  residues processed: 135
  average time/residue: 0.1069
  time to fit residues: 24.9672
Evaluate side-chains
  132 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 TRP
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  529 TRP
Chi-restraints excluded: chain B residue  660 MET
Chi-restraints excluded: chain B residue  699 THR
Chi-restraints excluded: chain B residue  809 SER
Chi-restraints excluded: chain B residue  910 GLN
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain C residue   42 MET
Chi-restraints excluded: chain C residue  374 ILE
Chi-restraints excluded: chain C residue  452 GLU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  953 THR
Chi-restraints excluded: chain C residue 1105 ILE
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 191 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 234 optimal weight:   20.0000
   chunk 97 optimal weight:    3.9990
   chunk 126 optimal weight:    0.0980
   chunk 55 optimal weight:    4.9990
   chunk 216 optimal weight:    5.9990
   chunk 233 optimal weight:    0.8980
   chunk 61 optimal weight:    8.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 714 HIS
B 910 GLN
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1018 HIS
** C1121 GLN ** 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 = 0.3871 r_free = 0.3871 target = 0.105719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.083114 restraints weight = 53708.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.083421 restraints weight = 33622.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.083918 restraints weight = 26400.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.084254 restraints weight = 22412.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.084400 restraints weight = 19961.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  19725  Z= 0.154
  Angle     :  0.569  11.607  26784  Z= 0.286
  Chirality :  0.041   0.141   2916
  Planarity :  0.004   0.056   3530
  Dihedral  :  4.547  23.276   2641
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.72 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.17), residues: 2392
  helix:  1.11 (0.15), residues: 1214
  sheet: -1.85 (0.35), residues: 209
  loop : -2.14 (0.19), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 135 
 TYR   0.011   0.001   TYR C 728 
 PHE   0.014   0.001   PHE B 127 
 TRP   0.012   0.001   TRP C 164 
 HIS   0.010   0.001   HIS C1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (19725)
  covalent geometry    : angle       0.56918 (26784)
  hydrogen bonds       : bond        0.04681 (  900)
  hydrogen bonds       : angle       4.45373 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  187 TRP cc_start: 0.7146 (OUTLIER) cc_final: 0.6350 (p90)
REVERT: B  518 MET cc_start: 0.8415 (mmm) cc_final: 0.8166 (mmm)
REVERT: B  727 MET cc_start: 0.6829 (mtt) cc_final: 0.6512 (mtt)
REVERT: C   96 MET cc_start: 0.8703 (tpp) cc_final: 0.8402 (ttm)
REVERT: C  452 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7592 (mp0)
REVERT: C  978 MET cc_start: 0.8914 (tmm) cc_final: 0.8392 (tmm)
REVERT: C 1031 MET cc_start: 0.9251 (tpp) cc_final: 0.8532 (tpp)
REVERT: C 1079 MET cc_start: 0.4273 (OUTLIER) cc_final: 0.3749 (tpt)
  outliers start: 36
  outliers final: 23
  residues processed: 143
  average time/residue: 0.1096
  time to fit residues: 26.6679
Evaluate side-chains
  141 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 TRP
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  529 TRP
Chi-restraints excluded: chain B residue  660 MET
Chi-restraints excluded: chain B residue  699 THR
Chi-restraints excluded: chain B residue  809 SER
Chi-restraints excluded: chain B residue  910 GLN
Chi-restraints excluded: chain B residue 1038 THR
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain C residue   42 MET
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  374 ILE
Chi-restraints excluded: chain C residue  452 GLU
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain C residue  752 ILE
Chi-restraints excluded: chain C residue  953 THR
Chi-restraints excluded: chain C residue 1018 HIS
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1079 MET
Chi-restraints excluded: chain C residue 1105 ILE
Chi-restraints excluded: chain D residue   26 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 116 optimal weight:    0.7980
   chunk 197 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0970
   chunk 31 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 216 optimal weight:    3.9990
   chunk 150 optimal weight:    0.9980
   chunk 83 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   chunk 182 optimal weight:    0.5980
   chunk 203 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 228 GLN
C 850 GLN
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1018 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.107692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.085970 restraints weight = 53185.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.085623 restraints weight = 33958.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086435 restraints weight = 25871.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.086946 restraints weight = 19972.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.087074 restraints weight = 17926.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054  19725  Z= 0.098
  Angle     :  0.528  10.143  26784  Z= 0.264
  Chirality :  0.039   0.157   2916
  Planarity :  0.004   0.056   3530
  Dihedral  :  4.334  23.390   2641
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.84 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.18), residues: 2392
  helix:  1.34 (0.15), residues: 1209
  sheet: -1.62 (0.35), residues: 206
  loop : -2.09 (0.19), residues: 977

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 728 
 TYR   0.010   0.001   TYR C1027 
 PHE   0.010   0.001   PHE B1135 
 TRP   0.012   0.001   TRP C 616 
 HIS   0.013   0.001   HIS C1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 (19725)
  covalent geometry    : angle       0.52822 (26784)
  hydrogen bonds       : bond        0.03806 (  900)
  hydrogen bonds       : angle       4.24959 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  187 TRP cc_start: 0.7112 (OUTLIER) cc_final: 0.6408 (p90)
REVERT: B  518 MET cc_start: 0.8221 (mmm) cc_final: 0.7976 (mmm)
REVERT: B 1098 MET cc_start: 0.7583 (mtp) cc_final: 0.7304 (mtp)
REVERT: C   96 MET cc_start: 0.8711 (tpp) cc_final: 0.8452 (ttm)
REVERT: C  452 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7434 (mp0)
REVERT: C  978 MET cc_start: 0.8790 (tmm) cc_final: 0.8350 (tmm)
REVERT: C 1079 MET cc_start: 0.4232 (OUTLIER) cc_final: 0.3698 (tpt)
REVERT: D  118 THR cc_start: 0.6019 (p) cc_final: 0.5764 (t)
  outliers start: 29
  outliers final: 16
  residues processed: 139
  average time/residue: 0.1057
  time to fit residues: 25.1360
Evaluate side-chains
  134 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  187 TRP
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  529 TRP
Chi-restraints excluded: chain B residue  660 MET
Chi-restraints excluded: chain B residue  809 SER
Chi-restraints excluded: chain B residue  888 LEU
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain C residue   42 MET
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  452 GLU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1079 MET
Chi-restraints excluded: chain C residue 1098 THR
Chi-restraints excluded: chain C residue 1105 ILE
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 158 optimal weight:    0.5980
   chunk 227 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 186 optimal weight:    1.9990
   chunk 200 optimal weight:    4.9990
   chunk 101 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 188 optimal weight:    5.9990
   chunk 229 optimal weight:   10.0000
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1018 HIS
** C1121 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 = 0.3694 r_free = 0.3694 target = 0.101603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.079178 restraints weight = 53910.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.078080 restraints weight = 37247.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.078823 restraints weight = 30226.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.079482 restraints weight = 23186.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.079624 restraints weight = 20574.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  19725  Z= 0.132
  Angle     :  0.552  10.952  26784  Z= 0.275
  Chirality :  0.040   0.144   2916
  Planarity :  0.004   0.055   3530
  Dihedral  :  4.339  22.586   2641
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.94 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.18), residues: 2392
  helix:  1.34 (0.15), residues: 1211
  sheet: -1.65 (0.35), residues: 205
  loop : -2.06 (0.19), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 135 
 TYR   0.012   0.001   TYR C 728 
 PHE   0.012   0.001   PHE B1135 
 TRP   0.011   0.001   TRP C 164 
 HIS   0.005   0.001   HIS C1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (19725)
  covalent geometry    : angle       0.55175 (26784)
  hydrogen bonds       : bond        0.04220 (  900)
  hydrogen bonds       : angle       4.29173 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 115
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  187 TRP cc_start: 0.7143 (OUTLIER) cc_final: 0.6360 (p90)
REVERT: B  518 MET cc_start: 0.8353 (mmm) cc_final: 0.8096 (mmm)
REVERT: B  910 GLN cc_start: 0.6244 (pt0) cc_final: 0.5520 (tm-30)
REVERT: B 1098 MET cc_start: 0.7621 (mtp) cc_final: 0.7335 (mtp)
REVERT: C   96 MET cc_start: 0.8715 (tpp) cc_final: 0.8465 (ttm)
REVERT: C  452 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7493 (mp0)
REVERT: C  978 MET cc_start: 0.8820 (tmm) cc_final: 0.8351 (tmm)
REVERT: C 1079 MET cc_start: 0.4233 (OUTLIER) cc_final: 0.3717 (tpt)
REVERT: D  118 THR cc_start: 0.6003 (p) cc_final: 0.5742 (t)
  outliers start: 37
  outliers final: 22
  residues processed: 140
  average time/residue: 0.1093
  time to fit residues: 26.3589
Evaluate side-chains
  138 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  187 TRP
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  529 TRP
Chi-restraints excluded: chain B residue  660 MET
Chi-restraints excluded: chain B residue  809 SER
Chi-restraints excluded: chain B residue  888 LEU
Chi-restraints excluded: chain B residue 1038 THR
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  374 ILE
Chi-restraints excluded: chain C residue  404 THR
Chi-restraints excluded: chain C residue  452 GLU
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain C residue  752 ILE
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue  953 THR
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1079 MET
Chi-restraints excluded: chain C residue 1098 THR
Chi-restraints excluded: chain C residue 1105 ILE
Chi-restraints excluded: chain C residue 1112 PHE
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 219 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 215 optimal weight:    6.9990
   chunk 198 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0970
   chunk 185 optimal weight:    6.9990
   chunk 223 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 130 optimal weight:   10.0000
   overall best weight:    4.2186

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

Flipped N/Q/H residues before XYZ refinement:
B 834 HIS
B 910 GLN
B1072 HIS
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1018 HIS
** C1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.097586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.074823 restraints weight = 54073.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.074285 restraints weight = 36571.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.074833 restraints weight = 30910.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.075223 restraints weight = 23738.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.075480 restraints weight = 21456.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080  19725  Z= 0.267
  Angle     :  0.706  15.966  26784  Z= 0.354
  Chirality :  0.044   0.148   2916
  Planarity :  0.005   0.056   3530
  Dihedral  :  4.930  25.158   2641
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.81 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.17), residues: 2392
  helix:  0.89 (0.15), residues: 1219
  sheet: -1.88 (0.35), residues: 202
  loop : -2.24 (0.19), residues: 971

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 728 
 TYR   0.020   0.002   TYR C 310 
 PHE   0.018   0.002   PHE C 694 
 TRP   0.018   0.002   TRP B 901 
 HIS   0.013   0.001   HIS B 689 

Details of bonding type rmsd
  covalent geometry    : bond        0.00626 (19725)
  covalent geometry    : angle       0.70600 (26784)
  hydrogen bonds       : bond        0.06189 (  900)
  hydrogen bonds       : angle       4.85577 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  187 TRP cc_start: 0.7520 (OUTLIER) cc_final: 0.6697 (p90)
REVERT: B  518 MET cc_start: 0.8543 (mmm) cc_final: 0.8327 (mmm)
REVERT: B  727 MET cc_start: 0.6134 (mtt) cc_final: 0.5932 (mtt)
REVERT: B 1098 MET cc_start: 0.7712 (mtp) cc_final: 0.7408 (mtp)
REVERT: C   96 MET cc_start: 0.8736 (tpp) cc_final: 0.8480 (ttm)
REVERT: C  446 GLN cc_start: 0.7932 (tp40) cc_final: 0.7448 (tp-100)
REVERT: C  978 MET cc_start: 0.8905 (tmm) cc_final: 0.8395 (tmm)
REVERT: C 1079 MET cc_start: 0.4347 (OUTLIER) cc_final: 0.4066 (tpt)
REVERT: C 1119 PHE cc_start: 0.6196 (m-10) cc_final: 0.5893 (m-10)
REVERT: D  118 THR cc_start: 0.5852 (p) cc_final: 0.5613 (t)
  outliers start: 37
  outliers final: 30
  residues processed: 142
  average time/residue: 0.1060
  time to fit residues: 25.4747
Evaluate side-chains
  145 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  187 TRP
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  529 TRP
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  809 SER
Chi-restraints excluded: chain B residue  888 LEU
Chi-restraints excluded: chain B residue  997 VAL
Chi-restraints excluded: chain B residue 1038 THR
Chi-restraints excluded: chain B residue 1138 VAL
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  374 ILE
Chi-restraints excluded: chain C residue  404 THR
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain C residue  752 ILE
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue  953 THR
Chi-restraints excluded: chain C residue 1018 HIS
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1079 MET
Chi-restraints excluded: chain C residue 1098 THR
Chi-restraints excluded: chain C residue 1105 ILE
Chi-restraints excluded: chain C residue 1112 PHE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 144 optimal weight:    0.9980
   chunk 102 optimal weight:    0.6980
   chunk 172 optimal weight:    4.9990
   chunk 199 optimal weight:   10.0000
   chunk 157 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 182 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 206 optimal weight:    6.9990
   chunk 198 optimal weight:    4.9990
   chunk 193 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 834 HIS
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1018 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.101791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.079383 restraints weight = 53277.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.078673 restraints weight = 36011.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.079428 restraints weight = 29188.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.080069 restraints weight = 22094.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.080165 restraints weight = 19562.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.072  19725  Z= 0.111
  Angle     :  0.561  11.184  26784  Z= 0.280
  Chirality :  0.040   0.182   2916
  Planarity :  0.004   0.056   3530
  Dihedral  :  4.479  24.017   2641
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 15.74 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.17), residues: 2392
  helix:  1.27 (0.15), residues: 1213
  sheet: -1.76 (0.35), residues: 209
  loop : -2.13 (0.19), residues: 970

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 728 
 TYR   0.015   0.001   TYR C1019 
 PHE   0.019   0.001   PHE C1119 
 TRP   0.030   0.001   TRP C 981 
 HIS   0.023   0.001   HIS C1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (19725)
  covalent geometry    : angle       0.56106 (26784)
  hydrogen bonds       : bond        0.04103 (  900)
  hydrogen bonds       : angle       4.36776 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  518 MET cc_start: 0.8352 (mmm) cc_final: 0.8060 (mmm)
REVERT: B 1098 MET cc_start: 0.7619 (mtp) cc_final: 0.7403 (mtp)
REVERT: C   96 MET cc_start: 0.8752 (tpp) cc_final: 0.8513 (ttm)
REVERT: C  978 MET cc_start: 0.8784 (tmm) cc_final: 0.8299 (tmm)
REVERT: C 1031 MET cc_start: 0.9029 (tpp) cc_final: 0.8070 (tpp)
REVERT: C 1079 MET cc_start: 0.4319 (OUTLIER) cc_final: 0.4000 (tpt)
REVERT: D  118 THR cc_start: 0.5778 (p) cc_final: 0.5557 (t)
  outliers start: 24
  outliers final: 21
  residues processed: 136
  average time/residue: 0.1056
  time to fit residues: 25.0039
Evaluate side-chains
  137 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  529 TRP
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  809 SER
Chi-restraints excluded: chain B residue  888 LEU
Chi-restraints excluded: chain B residue 1038 THR
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  404 THR
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue 1018 HIS
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1079 MET
Chi-restraints excluded: chain C residue 1093 LEU
Chi-restraints excluded: chain C residue 1098 THR
Chi-restraints excluded: chain C residue 1105 ILE
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 225 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 185 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 181 optimal weight:    1.9990
   chunk 191 optimal weight:    3.9990
   chunk 132 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 834 HIS
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1018 HIS
** C1121 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 = 0.3645 r_free = 0.3645 target = 0.098655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.076034 restraints weight = 52623.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.076121 restraints weight = 34714.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.076671 restraints weight = 27733.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.077020 restraints weight = 21320.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.077175 restraints weight = 19395.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  19725  Z= 0.237
  Angle     :  0.667  13.980  26784  Z= 0.333
  Chirality :  0.043   0.170   2916
  Planarity :  0.005   0.053   3530
  Dihedral  :  4.742  24.270   2641
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 15.54 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.17), residues: 2392
  helix:  1.05 (0.15), residues: 1214
  sheet: -1.93 (0.34), residues: 214
  loop : -2.21 (0.19), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 728 
 TYR   0.016   0.002   TYR C 310 
 PHE   0.017   0.002   PHE C1119 
 TRP   0.022   0.002   TRP C 981 
 HIS   0.015   0.001   HIS C1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 (19725)
  covalent geometry    : angle       0.66674 (26784)
  hydrogen bonds       : bond        0.05484 (  900)
  hydrogen bonds       : angle       4.67874 ( 2655)

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

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

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4784 Ramachandran restraints generated.
    2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  518 MET cc_start: 0.8496 (mmm) cc_final: 0.8281 (mmm)
REVERT: B 1098 MET cc_start: 0.7653 (mtp) cc_final: 0.7443 (mtp)
REVERT: C   96 MET cc_start: 0.8725 (tpp) cc_final: 0.8484 (ttm)
REVERT: C  446 GLN cc_start: 0.7922 (tp40) cc_final: 0.7460 (tp-100)
REVERT: C  978 MET cc_start: 0.8840 (tmm) cc_final: 0.8347 (tmm)
REVERT: C 1079 MET cc_start: 0.4506 (OUTLIER) cc_final: 0.4254 (tpt)
REVERT: D  118 THR cc_start: 0.5802 (p) cc_final: 0.5559 (t)
  outliers start: 33
  outliers final: 27
  residues processed: 137
  average time/residue: 0.1076
  time to fit residues: 25.3123
Evaluate side-chains
  143 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  529 TRP
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  809 SER
Chi-restraints excluded: chain B residue  888 LEU
Chi-restraints excluded: chain B residue 1038 THR
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain C residue   34 MET
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  374 ILE
Chi-restraints excluded: chain C residue  404 THR
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue 1018 HIS
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1079 MET
Chi-restraints excluded: chain C residue 1093 LEU
Chi-restraints excluded: chain C residue 1098 THR
Chi-restraints excluded: chain C residue 1105 ILE
Chi-restraints excluded: chain C residue 1112 PHE
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 239
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 87 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 181 optimal weight:    0.9980
   chunk 124 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 154 optimal weight:    0.9990
   chunk 137 optimal weight:    1.9990
   chunk 217 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 213 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 834 HIS
** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1018 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.101874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.079142 restraints weight = 53579.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.078533 restraints weight = 35244.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.079356 restraints weight = 27848.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.079681 restraints weight = 22522.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.079947 restraints weight = 19645.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  19725  Z= 0.109
  Angle     :  0.558  11.487  26784  Z= 0.279
  Chirality :  0.040   0.169   2916
  Planarity :  0.004   0.056   3530
  Dihedral  :  4.451  24.252   2641
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 16.03 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.17), residues: 2392
  helix:  1.30 (0.15), residues: 1214
  sheet: -1.90 (0.34), residues: 200
  loop : -2.11 (0.19), residues: 978

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 728 
 TYR   0.009   0.001   TYR B1081 
 PHE   0.019   0.001   PHE C 789 
 TRP   0.022   0.001   TRP C 981 
 HIS   0.023   0.001   HIS C1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (19725)
  covalent geometry    : angle       0.55805 (26784)
  hydrogen bonds       : bond        0.04007 (  900)
  hydrogen bonds       : angle       4.32615 ( 2655)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2315.91 seconds
wall clock time: 42 minutes 19.04 seconds (2539.04 seconds total)