Starting phenix.real_space_refine
on Thu Mar  5 06:29:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kiy_22890/03_2026/7kiy_22890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kiy_22890/03_2026/7kiy_22890.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kiy_22890/03_2026/7kiy_22890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kiy_22890/03_2026/7kiy_22890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kiy_22890/03_2026/7kiy_22890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kiy_22890/03_2026/7kiy_22890.cif"
  }
  resolution = 2.92
  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=   0.001
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      98      5.16       5
     C   12931      2.51       5
     N    3169      2.21       5
     O    3672      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 143 residue(s): 0.03s

  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: 19870
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 9817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1169, 9817
          Classifications: {'peptide': 1169}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 25, 'TRANS': 1139}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 4308
          Classifications: {'peptide': 516}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 506}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 5745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 691, 5745
          Classifications: {'peptide': 691}
          Link IDs: {'CIS': 3, 'PTRANS': 28, 'TRANS': 659}
  Time building chain proxies: 3.99, per 1000 atoms: 0.20
  Number of scatterers: 19870
  At special positions: 0
  Unit cell: (162.12, 114.24, 156.24, 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      98     16.00
     O    3672      8.00
     N    3169      7.00
     C   12931      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 335 " - pdb=" SG  CYS A 363 " distance=1.59
    Simple disulfide: pdb=" SG  CYS A 409 " - pdb=" SG  CYS A 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 519 " - pdb=" SG  CYS A 547 " distance=2.30
    Simple disulfide: pdb=" SG  CYS A 523 " - pdb=" SG  CYS A 544 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1352 " - pdb=" SG  CYS A1355 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 233 " - pdb=" SG  CYS B 240 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 791 " - pdb=" SG  CYS B 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 157 " - pdb=" SG  CYS C 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 244 " - pdb=" SG  CYS C 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 262 " - pdb=" SG  CYS C 276 " distance=2.32
    Simple disulfide: pdb=" SG  CYS C 475 " - pdb=" SG  CYS C 536 " distance=2.21

  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: 1.93
  Conformation dependent library (CDL) restraints added in 770.1 milliseconds
  

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4636

  Finding SS restraints...
    Secondary structure from input PDB file:
      115 helices and 3 sheets defined
      58.8% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 66
      removed outlier: 3.778A  pdb=" N   SER A  63 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   MET A  64 " --> pdb=" O   GLN A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 87
      removed outlier: 3.515A  pdb=" N   LYS A  87 " --> pdb=" O   GLU A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 108
      removed outlier: 3.593A  pdb=" N   LYS A 107 " --> pdb=" O   ASP A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 147
    Processing helix  chain 'A' and resid 154 through 181
      removed outlier: 3.832A  pdb=" N   LYS A 158 " --> pdb=" O   ASP A 154 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A 171 " --> pdb=" O   LYS A 167 " (cutoff:3.500A)
      Proline residue:  A 175  - end of helix
      removed outlier: 4.196A  pdb=" N   GLN A 181 " --> pdb=" O   ASN A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 198
      removed outlier: 3.678A  pdb=" N   PHE A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   THR A 197 " --> pdb=" O   ASN A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 226
      removed outlier: 3.841A  pdb=" N   PHE A 214 " --> pdb=" O   ASP A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 3.656A  pdb=" N   THR A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LEU A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 233 through 238'
    Processing helix  chain 'A' and resid 260 through 274
      removed outlier: 3.832A  pdb=" N   MET A 264 " --> pdb=" O   ASN A 260 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR A 274 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.800A  pdb=" N   HIS A 281 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 301
    Processing helix  chain 'A' and resid 301 through 307
    Processing helix  chain 'A' and resid 315 through 320
      removed outlier: 3.587A  pdb=" N   LEU A 320 " --> pdb=" O   TRP A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 333
      removed outlier: 4.075A  pdb=" N   LYS A 329 " --> pdb=" O   SER A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 351
    Processing helix  chain 'A' and resid 352 through 354
      No H-bonds generated for 'chain 'A' and resid 352 through 354'
    Processing helix  chain 'A' and resid 361 through 385
      removed outlier: 3.935A  pdb=" N   GLN A 385 " --> pdb=" O   ILE A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 409
      removed outlier: 3.562A  pdb=" N   PHE A 407 " --> pdb=" O   TYR A 403 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   MET A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   CYS A 409 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 420
      removed outlier: 3.596A  pdb=" N   THR A 420 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 459
      removed outlier: 3.522A  pdb=" N   ASN A 451 " --> pdb=" O   ASN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 464 through 480
      removed outlier: 3.794A  pdb=" N   ASN A 480 " --> pdb=" O   THR A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 489
    Processing helix  chain 'A' and resid 490 through 491
      No H-bonds generated for 'chain 'A' and resid 490 through 491'
    Processing helix  chain 'A' and resid 492 through 503
      removed outlier: 3.608A  pdb=" N   TYR A 495 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ASN A 497 " --> pdb=" O   GLY A 494 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   ALA A 498 " --> pdb=" O   TYR A 495 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   VAL A 499 " --> pdb=" O   TYR A 496 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A 500 " --> pdb=" O   ASN A 497 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   MET A 501 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   PHE A 503 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 521
      removed outlier: 3.613A  pdb=" N   LEU A 516 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 524
      No H-bonds generated for 'chain 'A' and resid 522 through 524'
    Processing helix  chain 'A' and resid 542 through 555
      removed outlier: 3.580A  pdb=" N   LEU A 546 " --> pdb=" O   THR A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 574
      removed outlier: 3.523A  pdb=" N   LYS A 567 " --> pdb=" O   SER A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 599
      removed outlier: 3.557A  pdb=" N   SER A 599 " --> pdb=" O   SER A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 614
      removed outlier: 3.805A  pdb=" N   THR A 614 " --> pdb=" O   LEU A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
      removed outlier: 3.814A  pdb=" N   ILE A 619 " --> pdb=" O   PHE A 616 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   SER A 620 " --> pdb=" O   LYS A 617 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 616 through 620'
    Processing helix  chain 'A' and resid 623 through 632
      removed outlier: 3.851A  pdb=" N   ILE A 632 " --> pdb=" O   MET A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 675
    Processing helix  chain 'A' and resid 680 through 686
    Processing helix  chain 'A' and resid 693 through 699
      removed outlier: 3.795A  pdb=" N   GLN A 699 " --> pdb=" O   ASN A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 732
    Processing helix  chain 'A' and resid 738 through 742
    Processing helix  chain 'A' and resid 747 through 758
      removed outlier: 4.378A  pdb=" N   ASP A 751 " --> pdb=" O   TYR A 747 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER A 758 " --> pdb=" O   ASP A 754 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 786
      removed outlier: 3.716A  pdb=" N   TRP A 769 " --> pdb=" O   LYS A 765 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A 771 " --> pdb=" O   ASN A 767 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL A 772 " --> pdb=" O   GLN A 768 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU A 786 " --> pdb=" O   ASP A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 795
      removed outlier: 3.978A  pdb=" N   LEU A 793 " --> pdb=" O   HIS A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 819
    Processing helix  chain 'A' and resid 877 through 893
      removed outlier: 4.022A  pdb=" N   GLU A 881 " --> pdb=" O   GLU A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 916
      removed outlier: 3.745A  pdb=" N   GLN A 904 " --> pdb=" O   THR A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 961
      removed outlier: 3.868A  pdb=" N   ILE A 950 " --> pdb=" O   GLU A 946 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ILE A 952 " --> pdb=" O   ARG A 948 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ARG A 959 " --> pdb=" O   SER A 955 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR A 961 " --> pdb=" O   ALA A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 977
      removed outlier: 3.883A  pdb=" N   ALA A 967 " --> pdb=" O   LYS A 963 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ALA A 968 " --> pdb=" O   THR A 964 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   THR A 975 " --> pdb=" O   MET A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 987
    Processing helix  chain 'A' and resid 998 through 1022
      removed outlier: 3.902A  pdb=" N   ILE A1014 " --> pdb=" O   TYR A1010 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   LEU A1022 " --> pdb=" O   VAL A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1033
      removed outlier: 3.728A  pdb=" N   GLN A1033 " --> pdb=" O   PRO A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1056
      removed outlier: 3.837A  pdb=" N   ASN A1044 " --> pdb=" O   PHE A1040 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU A1056 " --> pdb=" O   MET A1052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1060 through 1071
      removed outlier: 4.004A  pdb=" N   LEU A1064 " --> pdb=" O   ASN A1060 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   CYS A1065 " --> pdb=" O   LEU A1061 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1148 through 1164
    Processing helix  chain 'A' and resid 1202 through 1224
      removed outlier: 3.596A  pdb=" N   CYS A1217 " --> pdb=" O   MET A1213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1231 through 1235
      removed outlier: 3.659A  pdb=" N   ILE A1235 " --> pdb=" O   ASN A1232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1240 through 1260
      removed outlier: 4.196A  pdb=" N   ARG A1244 " --> pdb=" O   ARG A1240 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS A1260 " --> pdb=" O   TYR A1256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1267 through 1294
      removed outlier: 3.891A  pdb=" N   LYS A1271 " --> pdb=" O   ASP A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1310 through 1322
      removed outlier: 4.074A  pdb=" N   ASN A1314 " --> pdb=" O   ASP A1310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1323 through 1325
      No H-bonds generated for 'chain 'A' and resid 1323 through 1325'
    Processing helix  chain 'A' and resid 1345 through 1350
    Processing helix  chain 'B' and resid 236 through 260
      removed outlier: 3.872A  pdb=" N   GLU B 245 " --> pdb=" O   SER B 241 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER B 246 " --> pdb=" O   ARG B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 265
      removed outlier: 3.943A  pdb=" N   LEU B 264 " --> pdb=" O   ILE B 260 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ASP B 265 " --> pdb=" O   PRO B 261 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 260 through 265'
    Processing helix  chain 'B' and resid 274 through 280
      removed outlier: 3.942A  pdb=" N   LYS B 278 " --> pdb=" O   GLU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 376
      removed outlier: 4.257A  pdb=" N   SER B 366 " --> pdb=" O   LYS B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 388
      removed outlier: 4.155A  pdb=" N   PHE B 385 " --> pdb=" O   ASP B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 405
      removed outlier: 3.686A  pdb=" N   ASN B 402 " --> pdb=" O   LEU B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 446
    Processing helix  chain 'B' and resid 494 through 504
      removed outlier: 4.062A  pdb=" N   TYR B 503 " --> pdb=" O   TYR B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 528
      removed outlier: 3.826A  pdb=" N   LEU B 520 " --> pdb=" O   ASP B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 555
    Processing helix  chain 'B' and resid 561 through 567
    Processing helix  chain 'B' and resid 568 through 569
      No H-bonds generated for 'chain 'B' and resid 568 through 569'
    Processing helix  chain 'B' and resid 570 through 572
      No H-bonds generated for 'chain 'B' and resid 570 through 572'
    Processing helix  chain 'B' and resid 573 through 588
      removed outlier: 3.667A  pdb=" N   HIS B 577 " --> pdb=" O   ASP B 573 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL B 578 " --> pdb=" O   PHE B 574 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LEU B 579 " --> pdb=" O   VAL B 575 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LYS B 587 " --> pdb=" O   ASN B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 609
      removed outlier: 3.721A  pdb=" N   THR B 593 " --> pdb=" O   ASN B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 658
      removed outlier: 3.688A  pdb=" N   ILE B 651 " --> pdb=" O   SER B 647 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE B 654 " --> pdb=" O   TYR B 650 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 700
      removed outlier: 3.625A  pdb=" N   LEU B 687 " --> pdb=" O   ASN B 683 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ALA B 688 " --> pdb=" O   ILE B 684 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ASN B 700 " --> pdb=" O   ALA B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 703
      No H-bonds generated for 'chain 'B' and resid 701 through 703'
    Processing helix  chain 'B' and resid 715 through 727
    Processing helix  chain 'B' and resid 739 through 755
      removed outlier: 3.693A  pdb=" N   SER B 743 " --> pdb=" O   PHE B 739 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TYR B 744 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 781 through 798
    Processing helix  chain 'B' and resid 810 through 829
      removed outlier: 3.877A  pdb=" N   ALA B 828 " --> pdb=" O   VAL B 824 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS B 829 " --> pdb=" O   THR B 825 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 854
      removed outlier: 3.568A  pdb=" N   LEU B 847 " --> pdb=" O   LEU B 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 859 through 870
      removed outlier: 4.053A  pdb=" N   LEU B 863 " --> pdb=" O   ILE B 859 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   SER B 870 " --> pdb=" O   ASN B 866 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 879 through 895
      removed outlier: 3.526A  pdb=" N   LYS B 884 " --> pdb=" O   SER B 880 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LYS B 895 " --> pdb=" O   LEU B 891 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 897 through 915
    Processing helix  chain 'C' and resid 33 through 49
      removed outlier: 3.517A  pdb=" N   LYS C  37 " --> pdb=" O   THR C  33 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR C  38 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU C  39 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 77
      removed outlier: 3.793A  pdb=" N   PHE C  70 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR C  71 " --> pdb=" O   PRO C  67 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TRP C  72 " --> pdb=" O   GLU C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 112
      removed outlier: 3.659A  pdb=" N   LYS C 110 " --> pdb=" O   SER C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 135
      removed outlier: 4.259A  pdb=" N   VAL C 120 " --> pdb=" O   PHE C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 187
      removed outlier: 3.526A  pdb=" N   LYS C 186 " --> pdb=" O   GLU C 183 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL C 187 " --> pdb=" O   GLU C 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 183 through 187'
    Processing helix  chain 'C' and resid 195 through 203
      removed outlier: 3.506A  pdb=" N   TYR C 203 " --> pdb=" O   ILE C 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 222
    Processing helix  chain 'C' and resid 239 through 244
      removed outlier: 3.557A  pdb=" N   GLU C 243 " --> pdb=" O   HIS C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 259
    Processing helix  chain 'C' and resid 274 through 284
      removed outlier: 3.586A  pdb=" N   LEU C 282 " --> pdb=" O   HIS C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 298
    Processing helix  chain 'C' and resid 371 through 377
    Processing helix  chain 'C' and resid 379 through 382
      removed outlier: 3.662A  pdb=" N   TYR C 382 " --> pdb=" O   ASP C 379 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 379 through 382'
    Processing helix  chain 'C' and resid 383 through 392
      removed outlier: 3.534A  pdb=" N   LYS C 389 " --> pdb=" O   PHE C 385 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LYS C 390 " --> pdb=" O   PHE C 386 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 407
    Processing helix  chain 'C' and resid 420 through 424
      removed outlier: 4.278A  pdb=" N   ASN C 423 " --> pdb=" O   GLN C 420 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   VAL C 424 " --> pdb=" O   CYS C 421 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 420 through 424'
    Processing helix  chain 'C' and resid 433 through 454
      removed outlier: 3.861A  pdb=" N   LEU C 454 " --> pdb=" O   GLU C 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 471 through 492
      removed outlier: 3.718A  pdb=" N   HIS C 481 " --> pdb=" O   LEU C 477 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL C 482 " --> pdb=" O   ILE C 478 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 503 through 514
      removed outlier: 4.296A  pdb=" N   TYR C 507 " --> pdb=" O   TYR C 503 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE C 508 " --> pdb=" O   THR C 504 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   HIS C 509 " --> pdb=" O   SER C 505 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER C 514 " --> pdb=" O   LYS C 510 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 515 through 518
      removed outlier: 3.971A  pdb=" N   LEU C 518 " --> pdb=" O   VAL C 515 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 515 through 518'
    Processing helix  chain 'C' and resid 529 through 536
    Processing helix  chain 'C' and resid 542 through 548
      removed outlier: 4.012A  pdb=" N   VAL C 546 " --> pdb=" O   HIS C 542 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 562 through 570
    Processing helix  chain 'C' and resid 577 through 591
      removed outlier: 3.899A  pdb=" N   TYR C 589 " --> pdb=" O   PHE C 585 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 595 through 620
      removed outlier: 3.667A  pdb=" N   LEU C 599 " --> pdb=" O   GLU C 595 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLU C 612 " --> pdb=" O   LEU C 608 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLU C 616 " --> pdb=" O   GLU C 612 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   CYS C 620 " --> pdb=" O   GLU C 616 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 622 through 630
    Processing helix  chain 'C' and resid 631 through 633
      No H-bonds generated for 'chain 'C' and resid 631 through 633'
    Processing helix  chain 'C' and resid 635 through 651
      removed outlier: 3.773A  pdb=" N   ASP C 640 " --> pdb=" O   PRO C 636 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ARG C 641 " --> pdb=" O   ASN C 637 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS C 651 " --> pdb=" O   ASP C 647 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 655 through 666
    Processing helix  chain 'C' and resid 672 through 690
      removed outlier: 3.510A  pdb=" N   THR C 678 " --> pdb=" O   GLU C 674 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ALA C 679 " --> pdb=" O   LYS C 675 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU C 680 " --> pdb=" O   VAL C 676 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 112
    Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 692
      removed outlier: 6.620A  pdb=" N   GLY A 871 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 148 through 150

    834 hydrogen bonds defined for protein.
    2454 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.65

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        1.09 -     1.25: 3208
        1.25 -     1.41: 5435
        1.41 -     1.56: 11535
        1.56 -     1.72: 4
        1.72 -     1.88: 158
  Bond restraints: 20340
  Sorted by residual:
  bond pdb=" C   SER C 479 "
       pdb=" O   SER C 479 "
    ideal  model  delta    sigma   weight residual
    1.237  1.095  0.142 1.31e-02 5.83e+03 1.17e+02
  bond pdb=" C   ILE C 476 "
       pdb=" O   ILE C 476 "
    ideal  model  delta    sigma   weight residual
    1.237  1.121  0.116 1.13e-02 7.83e+03 1.06e+02
  bond pdb=" C   LEU C 477 "
       pdb=" O   LEU C 477 "
    ideal  model  delta    sigma   weight residual
    1.236  1.111  0.125 1.29e-02 6.01e+03 9.38e+01
  bond pdb=" C   CYS A 547 "
       pdb=" O   CYS A 547 "
    ideal  model  delta    sigma   weight residual
    1.237  1.124  0.112 1.16e-02 7.43e+03 9.38e+01
  bond pdb=" CA  SER C 479 "
       pdb=" CB  SER C 479 "
    ideal  model  delta    sigma   weight residual
    1.531  1.382  0.149 1.56e-02 4.11e+03 9.14e+01
  ... (remaining 20335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.56: 27321
        5.56 -    11.12: 87
       11.12 -    16.68: 11
       16.68 -    22.24: 1
       22.24 -    27.80: 1
  Bond angle restraints: 27421
  Sorted by residual:
  angle pdb=" N   ILE A 520 "
        pdb=" CA  ILE A 520 "
        pdb=" C   ILE A 520 "
      ideal   model   delta    sigma   weight residual
     111.45  100.08   11.37 9.30e-01 1.16e+00 1.49e+02
  angle pdb=" CA  CYS C 536 "
        pdb=" CB  CYS C 536 "
        pdb=" SG  CYS C 536 "
      ideal   model   delta    sigma   weight residual
     114.40   86.60   27.80 2.30e+00 1.89e-01 1.46e+02
  angle pdb=" C   ILE A 520 "
        pdb=" CA  ILE A 520 "
        pdb=" CB  ILE A 520 "
      ideal   model   delta    sigma   weight residual
     111.92   97.77   14.15 1.31e+00 5.83e-01 1.17e+02
  angle pdb=" C   CYS C 475 "
        pdb=" CA  CYS C 475 "
        pdb=" CB  CYS C 475 "
      ideal   model   delta    sigma   weight residual
     110.88   94.38   16.50 1.57e+00 4.06e-01 1.10e+02
  angle pdb=" N   CYS C 536 "
        pdb=" CA  CYS C 536 "
        pdb=" C   CYS C 536 "
      ideal   model   delta    sigma   weight residual
     112.87  125.06  -12.19 1.20e+00 6.94e-01 1.03e+02
  ... (remaining 27416 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.16: 10982
       18.16 -    36.32: 1060
       36.32 -    54.48: 178
       54.48 -    72.65: 27
       72.65 -    90.81: 13
  Dihedral angle restraints: 12260
    sinusoidal: 5089
      harmonic: 7171
  Sorted by residual:
  dihedral pdb=" CA  TYR B 876 "
           pdb=" C   TYR B 876 "
           pdb=" N   GLY B 877 "
           pdb=" CA  GLY B 877 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -89.19  -90.81     0      5.00e+00 4.00e-02 3.30e+02
  dihedral pdb=" CA  TYR A  92 "
           pdb=" C   TYR A  92 "
           pdb=" N   PRO A  93 "
           pdb=" CA  PRO A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -112.77  -67.23     0      5.00e+00 4.00e-02 1.81e+02
  dihedral pdb=" CA  GLN B 535 "
           pdb=" C   GLN B 535 "
           pdb=" N   ASN B 536 "
           pdb=" CA  ASN B 536 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.58  -40.42     0      5.00e+00 4.00e-02 6.54e+01
  ... (remaining 12257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.173: 2953
       0.173 -    0.346: 14
       0.346 -    0.520: 5
       0.520 -    0.693: 0
       0.693 -    0.866: 1
  Chirality restraints: 2973
  Sorted by residual:
  chirality pdb=" CA  CYS A 363 "
            pdb=" N   CYS A 363 "
            pdb=" C   CYS A 363 "
            pdb=" CB  CYS A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.64    0.87 2.00e-01 2.50e+01 1.88e+01
  chirality pdb=" CA  SER B 880 "
            pdb=" N   SER B 880 "
            pdb=" C   SER B 880 "
            pdb=" CB  SER B 880 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.49e+00
  chirality pdb=" CA  GLN A 518 "
            pdb=" N   GLN A 518 "
            pdb=" C   GLN A 518 "
            pdb=" CB  GLN A 518 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.66e+00
  ... (remaining 2970 not shown)

  Planarity restraints: 3444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 870 "    0.028 2.00e-02 2.50e+03   6.04e-02 3.65e+01
        pdb=" C   SER B 870 "   -0.104 2.00e-02 2.50e+03
        pdb=" O   SER B 870 "    0.042 2.00e-02 2.50e+03
        pdb=" N   CYS B 871 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  92 "   -0.067 5.00e-02 4.00e+02   1.02e-01 1.66e+01
        pdb=" N   PRO A  93 "    0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 479 "    0.019 2.00e-02 2.50e+03   3.81e-02 1.45e+01
        pdb=" C   SER C 479 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   SER C 479 "    0.025 2.00e-02 2.50e+03
        pdb=" N   THR C 480 "    0.022 2.00e-02 2.50e+03
  ... (remaining 3441 not shown)

  Histogram of nonbonded interaction distances:
        1.37 -     2.07: 7
        2.07 -     2.78: 4673
        2.78 -     3.49: 26298
        3.49 -     4.19: 42656
        4.19 -     4.90: 78547
  Nonbonded interactions: 152181
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 879 "
            pdb=" CD1 LEU B 883 "
     model   vdw
     1.366 3.460
  nonbonded pdb=" O   ALA C 539 "
            pdb=" N   LEU C 541 "
     model   vdw
     1.716 3.120
  nonbonded pdb=" O   ILE B 878 "
            pdb=" CD2 LEU B 883 "
     model   vdw
     1.719 3.460
  nonbonded pdb=" CG2 ILE B 878 "
            pdb=" CG  LEU B 883 "
     model   vdw
     1.817 3.890
  nonbonded pdb=" CG2 ILE B 878 "
            pdb=" CD2 LEU B 883 "
     model   vdw
     1.960 3.880
  ... (remaining 152176 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.390
  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:             0.020
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     17.090
  Find NCS groups from input model:        0.080
  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:6.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
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      :  0.009   0.442  20351  Z= 0.496
  Angle     :  1.116  69.331  27443  Z= 0.613
  Chirality :  0.054   0.866   2973
  Planarity :  0.005   0.102   3444
  Dihedral  : 14.296  90.807   7591
  Min Nonbonded Distance : 1.366

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 15.68 %
    Favored  : 83.56 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  4.69 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.30 %
    Twisted Proline : 3.28 %
    Twisted General : 0.39 %

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: -4.17 (0.14), residues: 2354
  helix: -1.55 (0.13), residues: 1282
  sheet: -3.44 (0.61), residues: 54
  loop : -4.46 (0.14), residues: 1018

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 549 
 TYR   0.026   0.002   TYR A 659 
 PHE   0.024   0.002   PHE A 389 
 TRP   0.012   0.002   TRP B 827 
 HIS   0.006   0.001   HIS C 481 

Details of bonding type rmsd
  covalent geometry    : bond        0.00752 (20340)
  covalent geometry    : angle       0.92904 (27421)
  SS BOND              : bond        0.18797 (   11)
  SS BOND              : angle      21.83076 (   22)
  hydrogen bonds       : bond        0.15590 (  834)
  hydrogen bonds       : angle       5.91984 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 290
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 THR cc_start: 0.8579 (m) cc_final: 0.8265 (p)
REVERT: A  586 LYS cc_start: 0.8590 (mttt) cc_final: 0.8389 (mttp)
REVERT: A  798 ASN cc_start: 0.7884 (m-40) cc_final: 0.7582 (m-40)
REVERT: A 1156 PHE cc_start: 0.8560 (t80) cc_final: 0.8346 (t80)
REVERT: A 1206 MET cc_start: 0.8411 (mtm) cc_final: 0.8024 (mmp)
REVERT: B  815 MET cc_start: 0.8051 (mmm) cc_final: 0.7575 (mmt)
REVERT: B  873 ILE cc_start: 0.4140 (OUTLIER) cc_final: 0.3916 (mp)
REVERT: B  891 LEU cc_start: 0.8758 (tt) cc_final: 0.8462 (mp)
REVERT: C  158 ILE cc_start: 0.8238 (mt) cc_final: 0.7823 (mp)
REVERT: C  163 ILE cc_start: 0.8167 (pt) cc_final: 0.7939 (pp)
REVERT: C  196 MET cc_start: 0.8805 (mtp) cc_final: 0.8439 (mmp)
REVERT: C  230 GLN cc_start: 0.8005 (mt0) cc_final: 0.7624 (mt0)
  outliers start: 19
  outliers final: 10
  residues processed: 308
  average time/residue: 0.6213
  time to fit residues: 215.6987
Evaluate side-chains
  162 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 TYR
Chi-restraints excluded: chain A residue  518 GLN
Chi-restraints excluded: chain A residue  519 CYS
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain B residue  397 PHE
Chi-restraints excluded: chain B residue  873 ILE
Chi-restraints excluded: chain B residue  874 SER
Chi-restraints excluded: chain B residue  878 ILE
Chi-restraints excluded: chain C residue  179 GLN
Chi-restraints excluded: chain C residue  453 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 216 optimal weight:    1.9990
   chunk 98 optimal weight:    7.9990
   chunk 194 optimal weight:    5.9990
   chunk 227 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 235 optimal weight:    0.0980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 198 ASN
A 281 HIS
A 392 HIS
A 422 GLN
A 474 ASN
A 600 HIS
A 693 HIS
A 759 GLN
A 797 HIS
A1057 ASN
A1255 ASN
B 407 ASN
** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 536 ASN
B 700 ASN
B 755 HIS
B 781 HIS
C  76 HIS
C 166 ASN
C 181 ASN
C 330 GLN
C 481 HIS
C 527 ASN
C 542 HIS
C 635 HIS

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.112077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.073420 restraints weight = 48211.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 3.24
r_work: 0.3048 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  20351  Z= 0.148
  Angle     :  0.741  12.970  27443  Z= 0.386
  Chirality :  0.044   0.208   2973
  Planarity :  0.005   0.093   3444
  Dihedral  :  6.839  61.799   2620
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 15.12 %
    Favored  : 84.71 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.80 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.30 %
    Twisted Proline : 3.28 %
    Twisted General : 0.13 %

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: -2.79 (0.16), residues: 2354
  helix: -0.27 (0.14), residues: 1294
  sheet: -2.04 (0.83), residues: 34
  loop : -4.14 (0.15), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 396 
 TYR   0.030   0.001   TYR A1283 
 PHE   0.016   0.001   PHE A1212 
 TRP   0.020   0.001   TRP B 896 
 HIS   0.007   0.001   HIS C 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (20340)
  covalent geometry    : angle       0.73644 (27421)
  SS BOND              : bond        0.00842 (   11)
  SS BOND              : angle       2.91992 (   22)
  hydrogen bonds       : bond        0.04729 (  834)
  hydrogen bonds       : angle       4.33697 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 184
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  506 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8822 (mm-30)
REVERT: A  586 LYS cc_start: 0.8914 (mttt) cc_final: 0.8581 (mtmt)
REVERT: A 1206 MET cc_start: 0.8515 (mtm) cc_final: 0.7978 (mmp)
REVERT: B  354 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7123 (tm-30)
REVERT: B  401 LEU cc_start: 0.8302 (tp) cc_final: 0.8020 (pp)
REVERT: B  511 GLN cc_start: 0.7440 (pm20) cc_final: 0.6849 (mm-40)
REVERT: B  529 LYS cc_start: 0.8244 (tppt) cc_final: 0.7722 (pmtt)
REVERT: B  678 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.4871 (m-10)
REVERT: B  815 MET cc_start: 0.8433 (mmm) cc_final: 0.8213 (mmt)
REVERT: B  842 SER cc_start: 0.8260 (m) cc_final: 0.7970 (t)
REVERT: B  891 LEU cc_start: 0.8653 (tt) cc_final: 0.8414 (mp)
REVERT: C  127 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8556 (tm-30)
REVERT: C  158 ILE cc_start: 0.8141 (mt) cc_final: 0.7919 (mt)
REVERT: C  163 ILE cc_start: 0.8023 (pt) cc_final: 0.7820 (pp)
REVERT: C  196 MET cc_start: 0.8893 (mtp) cc_final: 0.8512 (mmp)
REVERT: C  210 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7810 (tt0)
REVERT: C  230 GLN cc_start: 0.8067 (mt0) cc_final: 0.7791 (mt0)
REVERT: C  699 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7456 (tm-30)
  outliers start: 51
  outliers final: 23
  residues processed: 222
  average time/residue: 0.5398
  time to fit residues: 137.4253
Evaluate side-chains
  175 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 TYR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue 1207 GLU
Chi-restraints excluded: chain A residue 1237 SER
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  370 LYS
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  678 TYR
Chi-restraints excluded: chain C residue   26 ASP
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  474 LEU
Chi-restraints excluded: chain C residue  698 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 135 optimal weight:    0.0370
   chunk 129 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9980
   chunk 209 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 211 optimal weight:    6.9990
   chunk 200 optimal weight:    0.7980
   chunk 172 optimal weight:    3.9990
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
A 803 ASN
A1057 ASN
B 515 HIS
B 700 ASN
B 854 ASN
C 248 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.113264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.074416 restraints weight = 48250.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 3.28
r_work: 0.3078 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  20351  Z= 0.125
  Angle     :  0.672  12.774  27443  Z= 0.350
  Chirality :  0.042   0.195   2973
  Planarity :  0.004   0.093   3444
  Dihedral  :  6.150  57.955   2603
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 15.00 %
    Favored  : 84.92 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.36 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.26 %
    Twisted Proline : 3.28 %
    Twisted General : 0.13 %

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: -2.02 (0.17), residues: 2354
  helix:  0.47 (0.15), residues: 1292
  sheet: -2.69 (0.87), residues: 34
  loop : -3.90 (0.16), residues: 1028

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 396 
 TYR   0.030   0.001   TYR A1008 
 PHE   0.026   0.001   PHE A1212 
 TRP   0.018   0.001   TRP B 896 
 HIS   0.004   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (20340)
  covalent geometry    : angle       0.66881 (27421)
  SS BOND              : bond        0.00690 (   11)
  SS BOND              : angle       2.44317 (   22)
  hydrogen bonds       : bond        0.04038 (  834)
  hydrogen bonds       : angle       4.10598 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 178
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 LYS cc_start: 0.9037 (tmtt) cc_final: 0.8762 (tptp)
REVERT: A  506 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8825 (mm-30)
REVERT: A  537 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8526 (tt)
REVERT: A  661 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5817 (mmm160)
REVERT: A 1206 MET cc_start: 0.8633 (mtm) cc_final: 0.8153 (mmp)
REVERT: A 1213 MET cc_start: 0.6415 (mmm) cc_final: 0.6125 (mmm)
REVERT: A 1251 LYS cc_start: 0.9026 (tppt) cc_final: 0.8807 (tppt)
REVERT: A 1280 MET cc_start: 0.8676 (mtp) cc_final: 0.8218 (mmm)
REVERT: A 1301 MET cc_start: 0.0489 (OUTLIER) cc_final: 0.0205 (tpt)
REVERT: A 1325 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8937 (mtpt)
REVERT: B  354 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7294 (tm-30)
REVERT: B  390 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7803 (m-30)
REVERT: B  401 LEU cc_start: 0.8324 (tp) cc_final: 0.8056 (pp)
REVERT: B  511 GLN cc_start: 0.7458 (pm20) cc_final: 0.6884 (mm-40)
REVERT: B  529 LYS cc_start: 0.8242 (tppt) cc_final: 0.7547 (pptt)
REVERT: B  815 MET cc_start: 0.8425 (mmm) cc_final: 0.8197 (mmt)
REVERT: C  127 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8523 (tm-30)
REVERT: C  196 MET cc_start: 0.8885 (mtp) cc_final: 0.8553 (mmp)
REVERT: C  210 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7712 (mt0)
REVERT: C  699 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7562 (tm-30)
  outliers start: 55
  outliers final: 19
  residues processed: 215
  average time/residue: 0.5243
  time to fit residues: 130.3340
Evaluate side-chains
  171 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 TYR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue 1207 GLU
Chi-restraints excluded: chain A residue 1301 MET
Chi-restraints excluded: chain A residue 1325 LYS
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  370 LYS
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  610 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0570
   chunk 226 optimal weight:    0.2980
   chunk 7 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 206 optimal weight:    0.7980
   chunk 104 optimal weight:    0.4980
   chunk 205 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 198 optimal weight:    5.9990
   chunk 211 optimal weight:    1.9990
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 690 GLN
C 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.113973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.075489 restraints weight = 48461.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 3.28
r_work: 0.3100 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  20351  Z= 0.118
  Angle     :  0.659  14.283  27443  Z= 0.338
  Chirality :  0.041   0.200   2973
  Planarity :  0.004   0.094   3444
  Dihedral  :  5.910  56.615   2603
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 14.40 %
    Favored  : 85.51 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.42 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.26 %
    Twisted Proline : 3.28 %
    Twisted General : 0.13 %

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: -1.63 (0.17), residues: 2354
  helix:  0.80 (0.15), residues: 1299
  sheet: -2.53 (0.89), residues: 34
  loop : -3.78 (0.16), residues: 1021

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 396 
 TYR   0.052   0.001   TYR A1283 
 PHE   0.031   0.001   PHE A1212 
 TRP   0.021   0.001   TRP B 896 
 HIS   0.003   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (20340)
  covalent geometry    : angle       0.65639 (27421)
  SS BOND              : bond        0.00481 (   11)
  SS BOND              : angle       2.16805 (   22)
  hydrogen bonds       : bond        0.03671 (  834)
  hydrogen bonds       : angle       4.01294 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 171
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.8491 (tp30) cc_final: 0.8276 (tp30)
REVERT: A  226 LYS cc_start: 0.9057 (tmtt) cc_final: 0.8760 (tmmt)
REVERT: A  506 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8802 (mm-30)
REVERT: A  537 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8418 (tt)
REVERT: A  661 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.5774 (mmm160)
REVERT: A  803 ASN cc_start: 0.8682 (t0) cc_final: 0.8420 (t0)
REVERT: A  816 TYR cc_start: 0.9105 (t80) cc_final: 0.8776 (t80)
REVERT: A 1206 MET cc_start: 0.8668 (mtm) cc_final: 0.8147 (mmp)
REVERT: A 1251 LYS cc_start: 0.9034 (tppt) cc_final: 0.8751 (tppt)
REVERT: A 1280 MET cc_start: 0.8734 (mtp) cc_final: 0.8192 (mmm)
REVERT: A 1325 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8913 (mtpt)
REVERT: B  276 PHE cc_start: 0.6623 (t80) cc_final: 0.6291 (t80)
REVERT: B  354 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7215 (tm-30)
REVERT: B  390 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7912 (m-30)
REVERT: B  401 LEU cc_start: 0.8266 (tp) cc_final: 0.8038 (pp)
REVERT: B  511 GLN cc_start: 0.7448 (pm20) cc_final: 0.6875 (mm-40)
REVERT: B  529 LYS cc_start: 0.8230 (tppt) cc_final: 0.7552 (pptt)
REVERT: B  677 LEU cc_start: 0.6179 (tt) cc_final: 0.5976 (mt)
REVERT: B  815 MET cc_start: 0.8454 (mmm) cc_final: 0.8149 (mmt)
REVERT: B  883 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4603 (tt)
REVERT: B  886 MET cc_start: 0.1796 (tmt) cc_final: 0.1148 (tpt)
REVERT: C  127 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8616 (tm-30)
REVERT: C  158 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8020 (mp)
REVERT: C  180 LEU cc_start: 0.8212 (tp) cc_final: 0.7995 (tp)
REVERT: C  196 MET cc_start: 0.8886 (mtp) cc_final: 0.8563 (mmp)
REVERT: C  210 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7677 (mm110)
REVERT: C  229 VAL cc_start: 0.6784 (OUTLIER) cc_final: 0.6545 (m)
REVERT: C  303 PHE cc_start: 0.7391 (m-80) cc_final: 0.7104 (t80)
REVERT: C  699 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7526 (tm-30)
  outliers start: 58
  outliers final: 18
  residues processed: 214
  average time/residue: 0.5297
  time to fit residues: 131.2412
Evaluate side-chains
  179 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue 1325 LYS
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  723 MET
Chi-restraints excluded: chain B residue  857 GLU
Chi-restraints excluded: chain B residue  883 LEU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  610 ILE
Chi-restraints excluded: chain C residue  698 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 233 optimal weight:    0.6980
   chunk 183 optimal weight:    0.2980
   chunk 154 optimal weight:   10.0000
   chunk 221 optimal weight:    0.0370
   chunk 62 optimal weight:    0.9980
   chunk 161 optimal weight:    3.9990
   chunk 181 optimal weight:    0.9990
   chunk 203 optimal weight:    4.9990
   chunk 184 optimal weight:    0.0010
   chunk 218 optimal weight:    2.9990
   overall best weight:    0.4064

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

Flipped N/Q/H residues before XYZ refinement:
C 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.114489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.076369 restraints weight = 48347.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 3.28
r_work: 0.3114 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.063  20351  Z= 0.112
  Angle     :  0.647  13.614  27443  Z= 0.330
  Chirality :  0.040   0.208   2973
  Planarity :  0.004   0.098   3444
  Dihedral  :  5.556  51.530   2601
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.49 %
    Favored  : 85.51 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.11 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.26 %
    Twisted Proline : 3.28 %
    Twisted General : 0.13 %

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: -1.32 (0.18), residues: 2354
  helix:  1.12 (0.15), residues: 1280
  sheet: -1.56 (1.02), residues: 24
  loop : -3.67 (0.16), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 396 
 TYR   0.029   0.001   TYR A 747 
 PHE   0.032   0.001   PHE A1212 
 TRP   0.024   0.001   TRP B 896 
 HIS   0.004   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (20340)
  covalent geometry    : angle       0.64477 (27421)
  SS BOND              : bond        0.00394 (   11)
  SS BOND              : angle       1.89292 (   22)
  hydrogen bonds       : bond        0.03514 (  834)
  hydrogen bonds       : angle       3.93747 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 173
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.8524 (tp30) cc_final: 0.8228 (tp30)
REVERT: A  506 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8801 (mm-30)
REVERT: A  537 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8336 (tt)
REVERT: A  803 ASN cc_start: 0.8744 (t0) cc_final: 0.8516 (t0)
REVERT: A  942 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8692 (pttm)
REVERT: A 1206 MET cc_start: 0.8542 (mtm) cc_final: 0.8192 (mmp)
REVERT: A 1249 PHE cc_start: 0.7713 (t80) cc_final: 0.6784 (t80)
REVERT: A 1251 LYS cc_start: 0.9107 (tppt) cc_final: 0.8826 (tppt)
REVERT: A 1280 MET cc_start: 0.8793 (mtp) cc_final: 0.8472 (mtp)
REVERT: A 1325 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8912 (mtpt)
REVERT: B  276 PHE cc_start: 0.6700 (t80) cc_final: 0.6491 (t80)
REVERT: B  354 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7244 (tm-30)
REVERT: B  390 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7900 (m-30)
REVERT: B  401 LEU cc_start: 0.8310 (tp) cc_final: 0.8092 (pp)
REVERT: B  420 ASN cc_start: 0.7838 (p0) cc_final: 0.7332 (p0)
REVERT: B  511 GLN cc_start: 0.7490 (pm20) cc_final: 0.6963 (mm-40)
REVERT: B  529 LYS cc_start: 0.8201 (tppt) cc_final: 0.7570 (pptt)
REVERT: B  677 LEU cc_start: 0.6241 (tt) cc_final: 0.6013 (mt)
REVERT: C   41 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8658 (m-30)
REVERT: C  127 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8612 (tm-30)
REVERT: C  158 ILE cc_start: 0.8312 (mt) cc_final: 0.8070 (mp)
REVERT: C  196 MET cc_start: 0.8872 (mtp) cc_final: 0.8597 (mmp)
REVERT: C  210 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7633 (mm110)
REVERT: C  229 VAL cc_start: 0.6621 (OUTLIER) cc_final: 0.5913 (m)
REVERT: C  230 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8078 (mp10)
REVERT: C  303 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6999 (t80)
REVERT: C  409 ASP cc_start: 0.8095 (t0) cc_final: 0.7817 (t0)
REVERT: C  699 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7458 (tm-30)
  outliers start: 48
  outliers final: 23
  residues processed: 210
  average time/residue: 0.5200
  time to fit residues: 126.5385
Evaluate side-chains
  184 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  942 LYS
Chi-restraints excluded: chain A residue 1325 LYS
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  723 MET
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain C residue   41 ASP
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  230 GLN
Chi-restraints excluded: chain C residue  303 PHE
Chi-restraints excluded: chain C residue  634 ILE
Chi-restraints excluded: chain C residue  698 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 150 optimal weight:    9.9990
   chunk 182 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 186 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 106 optimal weight:    6.9990
   chunk 196 optimal weight:    0.5980
   chunk 94 optimal weight:    0.8980
   chunk 167 optimal weight:    0.9980
   overall best weight:    1.4382

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

Flipped N/Q/H residues before XYZ refinement:
B 801 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.111952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.073370 restraints weight = 48269.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.26
r_work: 0.3054 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  20351  Z= 0.148
  Angle     :  0.678  17.230  27443  Z= 0.348
  Chirality :  0.042   0.183   2973
  Planarity :  0.004   0.100   3444
  Dihedral  :  5.570  51.502   2601
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.61 %
    Favored  : 85.39 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.10 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.26 %
    Twisted Proline : 3.28 %
    Twisted General : 0.09 %

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: -1.22 (0.18), residues: 2354
  helix:  1.16 (0.15), residues: 1288
  sheet: -1.49 (1.03), residues: 24
  loop : -3.60 (0.16), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 211 
 TYR   0.045   0.001   TYR A1283 
 PHE   0.040   0.001   PHE A1212 
 TRP   0.029   0.001   TRP B 896 
 HIS   0.005   0.001   HIS C 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (20340)
  covalent geometry    : angle       0.67634 (27421)
  SS BOND              : bond        0.00470 (   11)
  SS BOND              : angle       2.01486 (   22)
  hydrogen bonds       : bond        0.04412 (  834)
  hydrogen bonds       : angle       3.98760 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 164
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.8621 (tp30) cc_final: 0.8275 (tp30)
REVERT: A  506 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8800 (mm-30)
REVERT: A  537 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8507 (tt)
REVERT: A  803 ASN cc_start: 0.8825 (t0) cc_final: 0.8590 (t0)
REVERT: A  816 TYR cc_start: 0.9261 (t80) cc_final: 0.8988 (t80)
REVERT: A  945 LYS cc_start: 0.9077 (tppt) cc_final: 0.8811 (tppp)
REVERT: A  963 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9017 (tttm)
REVERT: A 1206 MET cc_start: 0.8579 (mtm) cc_final: 0.8218 (mmp)
REVERT: A 1251 LYS cc_start: 0.9086 (tppt) cc_final: 0.8834 (tppt)
REVERT: A 1280 MET cc_start: 0.8733 (mtp) cc_final: 0.8154 (mmm)
REVERT: A 1325 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8884 (mtpt)
REVERT: B  276 PHE cc_start: 0.6724 (t80) cc_final: 0.6510 (t80)
REVERT: B  349 ILE cc_start: 0.5856 (OUTLIER) cc_final: 0.5456 (mt)
REVERT: B  390 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7914 (m-30)
REVERT: B  420 ASN cc_start: 0.7849 (p0) cc_final: 0.7378 (p0)
REVERT: B  511 GLN cc_start: 0.7509 (pm20) cc_final: 0.7267 (mp10)
REVERT: B  529 LYS cc_start: 0.8197 (tppt) cc_final: 0.7558 (pptt)
REVERT: B  677 LEU cc_start: 0.6280 (tt) cc_final: 0.6042 (mt)
REVERT: B  730 HIS cc_start: 0.5041 (m-70) cc_final: 0.4206 (m90)
REVERT: C  158 ILE cc_start: 0.8411 (mt) cc_final: 0.8152 (mp)
REVERT: C  196 MET cc_start: 0.8904 (mtp) cc_final: 0.8628 (mmp)
REVERT: C  303 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6897 (t80)
REVERT: C  699 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7502 (tm-30)
  outliers start: 55
  outliers final: 25
  residues processed: 207
  average time/residue: 0.5042
  time to fit residues: 121.1028
Evaluate side-chains
  179 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  916 THR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue 1325 LYS
Chi-restraints excluded: chain A residue 1328 MET
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  370 LYS
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  723 MET
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  303 PHE
Chi-restraints excluded: chain C residue  610 ILE
Chi-restraints excluded: chain C residue  698 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 207 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 215 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 127 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 118 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 388 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.113159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.074848 restraints weight = 48475.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 3.28
r_work: 0.3078 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  20351  Z= 0.123
  Angle     :  0.672  13.487  27443  Z= 0.342
  Chirality :  0.041   0.183   2973
  Planarity :  0.004   0.094   3444
  Dihedral  :  5.466  50.457   2601
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.19 %
    Favored  : 85.81 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 18.50 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.30 %
    Twisted Proline : 3.28 %
    Twisted General : 0.04 %

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: -1.05 (0.18), residues: 2354
  helix:  1.31 (0.15), residues: 1286
  sheet: -1.50 (1.02), residues: 24
  loop : -3.52 (0.16), residues: 1044

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 396 
 TYR   0.026   0.001   TYR A 747 
 PHE   0.026   0.001   PHE A1212 
 TRP   0.020   0.001   TRP B 896 
 HIS   0.004   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (20340)
  covalent geometry    : angle       0.66936 (27421)
  SS BOND              : bond        0.00473 (   11)
  SS BOND              : angle       2.14278 (   22)
  hydrogen bonds       : bond        0.03839 (  834)
  hydrogen bonds       : angle       3.95493 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 163
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.8629 (tp30) cc_final: 0.8262 (tp30)
REVERT: A  506 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8808 (mm-30)
REVERT: A  537 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8437 (tt)
REVERT: A  803 ASN cc_start: 0.8855 (t0) cc_final: 0.8640 (t0)
REVERT: A  816 TYR cc_start: 0.9220 (t80) cc_final: 0.8912 (t80)
REVERT: A  868 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8142 (mm)
REVERT: A  945 LYS cc_start: 0.9097 (tppt) cc_final: 0.8848 (tppp)
REVERT: A  963 LYS cc_start: 0.9342 (mmmt) cc_final: 0.9007 (tttm)
REVERT: A 1160 PHE cc_start: 0.8477 (t80) cc_final: 0.8172 (t80)
REVERT: A 1206 MET cc_start: 0.8599 (mtm) cc_final: 0.8232 (mmp)
REVERT: A 1249 PHE cc_start: 0.7794 (t80) cc_final: 0.6821 (t80)
REVERT: A 1251 LYS cc_start: 0.9102 (tppt) cc_final: 0.8880 (tppt)
REVERT: A 1267 ASP cc_start: 0.8323 (p0) cc_final: 0.7864 (m-30)
REVERT: A 1280 MET cc_start: 0.8771 (mtp) cc_final: 0.8379 (mtp)
REVERT: A 1325 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8893 (mtpt)
REVERT: B  349 ILE cc_start: 0.5615 (OUTLIER) cc_final: 0.5314 (mt)
REVERT: B  390 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7868 (m-30)
REVERT: B  420 ASN cc_start: 0.7790 (p0) cc_final: 0.7370 (p0)
REVERT: B  511 GLN cc_start: 0.7525 (pm20) cc_final: 0.7259 (mp10)
REVERT: B  529 LYS cc_start: 0.8200 (tppt) cc_final: 0.7531 (pptt)
REVERT: B  842 SER cc_start: 0.8394 (m) cc_final: 0.8063 (t)
REVERT: B  896 TRP cc_start: 0.6819 (m-90) cc_final: 0.6619 (m-90)
REVERT: C  158 ILE cc_start: 0.8361 (mt) cc_final: 0.8103 (mp)
REVERT: C  196 MET cc_start: 0.8928 (mtp) cc_final: 0.8725 (mmp)
REVERT: C  210 GLN cc_start: 0.8119 (tp-100) cc_final: 0.7774 (mm110)
REVERT: C  303 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6868 (t80)
REVERT: C  414 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7526 (tp30)
REVERT: C  699 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7488 (tm-30)
  outliers start: 57
  outliers final: 25
  residues processed: 209
  average time/residue: 0.4565
  time to fit residues: 111.8982
Evaluate side-chains
  182 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  636 ASP
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  777 ILE
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue 1325 LYS
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  276 PHE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  303 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  474 LEU
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  610 ILE
Chi-restraints excluded: chain C residue  634 ILE
Chi-restraints excluded: chain C residue  698 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 232 optimal weight:    3.9990
   chunk 152 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 130 optimal weight:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 116 optimal weight:    5.9990
   chunk 156 optimal weight:    8.9990
   chunk 135 optimal weight:   20.0000
   chunk 166 optimal weight:    6.9990
   chunk 99 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 249 ASN
A 285 HIS
** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 700 ASN
C 118 ASN
** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 230 GLN
C 468 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.106724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.067971 restraints weight = 48796.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 3.18
r_work: 0.2933 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.075  20351  Z= 0.351
  Angle     :  0.868  16.600  27443  Z= 0.451
  Chirality :  0.051   0.302   2973
  Planarity :  0.005   0.110   3444
  Dihedral  :  6.218  57.698   2601
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.38 %
    Favored  : 84.49 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.84 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.30 %
    Twisted Proline : 3.28 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.17), residues: 2354
  helix:  0.66 (0.14), residues: 1318
  sheet: -1.26 (1.10), residues: 24
  loop : -3.70 (0.16), residues: 1012

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 549 
 TYR   0.047   0.002   TYR A1283 
 PHE   0.068   0.003   PHE B 276 
 TRP   0.017   0.002   TRP B 896 
 HIS   0.007   0.002   HIS C 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00829 (20340)
  covalent geometry    : angle       0.86440 (27421)
  SS BOND              : bond        0.00738 (   11)
  SS BOND              : angle       2.85056 (   22)
  hydrogen bonds       : bond        0.06968 (  834)
  hydrogen bonds       : angle       4.50511 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 154
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.8682 (tp30) cc_final: 0.8360 (tp30)
REVERT: A  506 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8818 (mm-30)
REVERT: A  537 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.8916 (tt)
REVERT: A  586 LYS cc_start: 0.9066 (mttt) cc_final: 0.8747 (mtmt)
REVERT: A  803 ASN cc_start: 0.8982 (t0) cc_final: 0.8764 (t0)
REVERT: A  945 LYS cc_start: 0.9087 (tppt) cc_final: 0.8809 (tppp)
REVERT: A  963 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9162 (tttm)
REVERT: A 1015 MET cc_start: 0.8742 (mpt) cc_final: 0.8148 (tpt)
REVERT: A 1023 LEU cc_start: 0.8103 (mt) cc_final: 0.7737 (mt)
REVERT: A 1206 MET cc_start: 0.8578 (mtm) cc_final: 0.8226 (mmp)
REVERT: A 1280 MET cc_start: 0.8787 (mtp) cc_final: 0.8237 (mmm)
REVERT: A 1321 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8464 (mm-30)
REVERT: A 1325 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8837 (mtpt)
REVERT: B  276 PHE cc_start: 0.6201 (t80) cc_final: 0.5932 (t80)
REVERT: B  349 ILE cc_start: 0.5778 (OUTLIER) cc_final: 0.5476 (mt)
REVERT: B  390 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7903 (m-30)
REVERT: B  511 GLN cc_start: 0.7531 (pm20) cc_final: 0.7237 (mp10)
REVERT: B  700 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8924 (t0)
REVERT: C  127 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8565 (tm-30)
REVERT: C  158 ILE cc_start: 0.8634 (mt) cc_final: 0.8368 (mp)
REVERT: C  210 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7625 (mm110)
REVERT: C  303 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6942 (t80)
REVERT: C  699 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7735 (tm-30)
  outliers start: 49
  outliers final: 20
  residues processed: 195
  average time/residue: 0.5075
  time to fit residues: 114.7472
Evaluate side-chains
  164 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  636 ASP
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  901 SER
Chi-restraints excluded: chain A residue  916 THR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue 1325 LYS
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  700 ASN
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  303 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  610 ILE
Chi-restraints excluded: chain C residue  698 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 85 optimal weight:    0.1980
   chunk 68 optimal weight:    0.9980
   chunk 201 optimal weight:    0.8980
   chunk 223 optimal weight:    0.6980
   chunk 233 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 133 optimal weight:    5.9990
   chunk 149 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 232 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 524 HIS
A 753 HIS
C 154 HIS
C 166 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.111315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.072955 restraints weight = 48231.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 3.25
r_work: 0.3036 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  20351  Z= 0.134
  Angle     :  0.716  14.754  27443  Z= 0.367
  Chirality :  0.043   0.243   2973
  Planarity :  0.004   0.099   3444
  Dihedral  :  5.828  55.431   2601
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  : 13.89 %
    Favored  : 86.07 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 20.42 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.26 %
    Twisted Proline : 3.28 %
    Twisted General : 0.09 %

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: -1.22 (0.18), residues: 2354
  helix:  1.05 (0.15), residues: 1306
  sheet: -1.34 (1.05), residues: 24
  loop : -3.51 (0.17), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 396 
 TYR   0.026   0.001   TYR A 747 
 PHE   0.022   0.001   PHE A1156 
 TRP   0.034   0.001   TRP B 896 
 HIS   0.004   0.001   HIS B 811 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (20340)
  covalent geometry    : angle       0.71344 (27421)
  SS BOND              : bond        0.00524 (   11)
  SS BOND              : angle       2.22199 (   22)
  hydrogen bonds       : bond        0.04305 (  834)
  hydrogen bonds       : angle       4.08311 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.8606 (tp30) cc_final: 0.8300 (tp30)
REVERT: A  506 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8787 (mm-30)
REVERT: A  537 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8739 (tt)
REVERT: A  945 LYS cc_start: 0.9110 (tppt) cc_final: 0.8831 (tppp)
REVERT: A  963 LYS cc_start: 0.9335 (mmmt) cc_final: 0.9010 (tttm)
REVERT: A 1015 MET cc_start: 0.8777 (mpt) cc_final: 0.8212 (tpt)
REVERT: A 1023 LEU cc_start: 0.8037 (mt) cc_final: 0.7640 (mt)
REVERT: A 1206 MET cc_start: 0.8561 (mtm) cc_final: 0.8259 (mmp)
REVERT: A 1280 MET cc_start: 0.8858 (mtp) cc_final: 0.8338 (mmm)
REVERT: A 1325 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8867 (mtpt)
REVERT: B  276 PHE cc_start: 0.6596 (t80) cc_final: 0.6334 (t80)
REVERT: B  348 TYR cc_start: 0.5863 (t80) cc_final: 0.5407 (m-80)
REVERT: B  349 ILE cc_start: 0.5533 (OUTLIER) cc_final: 0.5063 (mt)
REVERT: B  390 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7890 (m-30)
REVERT: B  420 ASN cc_start: 0.7765 (p0) cc_final: 0.7411 (p0)
REVERT: B  511 GLN cc_start: 0.7587 (pm20) cc_final: 0.7308 (mp10)
REVERT: B  529 LYS cc_start: 0.8207 (tppt) cc_final: 0.7768 (pmtt)
REVERT: B  896 TRP cc_start: 0.6850 (m-90) cc_final: 0.6613 (m-90)
REVERT: C  158 ILE cc_start: 0.8331 (mt) cc_final: 0.8042 (mp)
REVERT: C  303 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7028 (t80)
REVERT: C  699 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7613 (tm-30)
  outliers start: 35
  outliers final: 19
  residues processed: 184
  average time/residue: 0.4973
  time to fit residues: 106.6804
Evaluate side-chains
  169 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  777 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1325 LYS
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  730 HIS
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  154 HIS
Chi-restraints excluded: chain C residue  303 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  610 ILE
Chi-restraints excluded: chain C residue  698 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 235 optimal weight:    0.3980
   chunk 59 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 168 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 155 optimal weight:    0.7980
   chunk 160 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 803 ASN
C 154 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.112062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.073780 restraints weight = 48913.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 3.28
r_work: 0.3063 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  20351  Z= 0.126
  Angle     :  0.696  14.822  27443  Z= 0.355
  Chirality :  0.042   0.181   2973
  Planarity :  0.004   0.100   3444
  Dihedral  :  5.576  51.846   2601
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.15 %
    Favored  : 85.85 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 21.05 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.30 %
    Twisted Proline : 3.28 %
    Twisted General : 0.04 %

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 (0.18), residues: 2354
  helix:  1.24 (0.15), residues: 1301
  sheet: -1.11 (1.09), residues: 24
  loop : -3.43 (0.17), residues: 1029

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 396 
 TYR   0.047   0.001   TYR A1283 
 PHE   0.045   0.001   PHE A1212 
 TRP   0.031   0.001   TRP B 896 
 HIS   0.005   0.001   HIS C 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (20340)
  covalent geometry    : angle       0.69339 (27421)
  SS BOND              : bond        0.00442 (   11)
  SS BOND              : angle       2.08944 (   22)
  hydrogen bonds       : bond        0.04025 (  834)
  hydrogen bonds       : angle       4.02846 ( 2454)

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

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

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4708 Ramachandran restraints generated.
    2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.8599 (tp30) cc_final: 0.8280 (tp30)
REVERT: A  456 MET cc_start: 0.9242 (tpp) cc_final: 0.8887 (mmm)
REVERT: A  506 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8797 (mm-30)
REVERT: A  537 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8600 (tt)
REVERT: A  800 TYR cc_start: 0.6380 (m-80) cc_final: 0.6120 (m-80)
REVERT: A  816 TYR cc_start: 0.9242 (t80) cc_final: 0.8978 (t80)
REVERT: A  945 LYS cc_start: 0.9121 (tppt) cc_final: 0.8888 (tppp)
REVERT: A  963 LYS cc_start: 0.9323 (mmmt) cc_final: 0.8990 (tttm)
REVERT: A 1015 MET cc_start: 0.8791 (mpt) cc_final: 0.8194 (tpt)
REVERT: A 1023 LEU cc_start: 0.8000 (mt) cc_final: 0.7600 (mt)
REVERT: A 1206 MET cc_start: 0.8553 (mtm) cc_final: 0.8259 (mmp)
REVERT: A 1280 MET cc_start: 0.8845 (mtp) cc_final: 0.8292 (mmm)
REVERT: A 1325 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8836 (mtpt)
REVERT: B  276 PHE cc_start: 0.6637 (t80) cc_final: 0.6331 (t80)
REVERT: B  348 TYR cc_start: 0.5864 (t80) cc_final: 0.5420 (m-80)
REVERT: B  349 ILE cc_start: 0.5622 (OUTLIER) cc_final: 0.5164 (mt)
REVERT: B  390 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7841 (m-30)
REVERT: B  420 ASN cc_start: 0.7727 (p0) cc_final: 0.7379 (p0)
REVERT: B  511 GLN cc_start: 0.7654 (pm20) cc_final: 0.7412 (mp10)
REVERT: B  529 LYS cc_start: 0.8200 (tppt) cc_final: 0.7770 (pmtt)
REVERT: B  896 TRP cc_start: 0.6917 (OUTLIER) cc_final: 0.6703 (m-90)
REVERT: C  158 ILE cc_start: 0.8345 (mt) cc_final: 0.8108 (mp)
REVERT: C  303 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6985 (t80)
REVERT: C  698 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8102 (tp)
REVERT: C  699 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7539 (tm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 177
  average time/residue: 0.4879
  time to fit residues: 100.8247
Evaluate side-chains
  169 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  636 ASP
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1325 LYS
Chi-restraints excluded: chain A residue 1352 CYS
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  896 TRP
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  303 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  610 ILE
Chi-restraints excluded: chain C residue  698 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 236
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 215 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 219 optimal weight:    0.0070
   chunk 115 optimal weight:    0.6980
   chunk 183 optimal weight:    5.9990
   chunk 217 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 189 optimal weight:    9.9990
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 154 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.113324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.075240 restraints weight = 48767.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 3.30
r_work: 0.3091 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  20351  Z= 0.121
  Angle     :  0.688  14.903  27443  Z= 0.350
  Chirality :  0.042   0.219   2973
  Planarity :  0.004   0.097   3444
  Dihedral  :  5.415  50.220   2601
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.72 %
    Favored  : 86.28 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 21.05 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.30 %
    Twisted Proline : 3.28 %
    Twisted General : 0.04 %

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: -0.88 (0.18), residues: 2354
  helix:  1.35 (0.15), residues: 1294
  sheet: -1.07 (1.12), residues: 24
  loop : -3.34 (0.17), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 661 
 TYR   0.026   0.001   TYR A1008 
 PHE   0.041   0.001   PHE A 703 
 TRP   0.031   0.001   TRP B 896 
 HIS   0.005   0.001   HIS B 811 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (20340)
  covalent geometry    : angle       0.68579 (27421)
  SS BOND              : bond        0.00389 (   11)
  SS BOND              : angle       1.96674 (   22)
  hydrogen bonds       : bond        0.03832 (  834)
  hydrogen bonds       : angle       3.96776 ( 2454)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7387.43 seconds
wall clock time: 126 minutes 21.10 seconds (7581.10 seconds total)