Starting phenix.real_space_refine
on Sat Jun 21 13:49:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8so9_40650/06_2025/8so9_40650.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8so9_40650/06_2025/8so9_40650.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8so9_40650/06_2025/8so9_40650.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8so9_40650/06_2025/8so9_40650.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8so9_40650/06_2025/8so9_40650.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8so9_40650/06_2025/8so9_40650.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.984
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: 5
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    7864      2.51       5
     N    2096      2.21       5
     O    2229      1.98       5
     H   12386      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 24636
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 16409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1008, 16409
          Classifications: {'peptide': 1008}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 962}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 8227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 8227
          Classifications: {'peptide': 515}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 489}
          Chain breaks: 8
  Time building chain proxies: 10.87, per 1000 atoms: 0.44
  Number of scatterers: 24636
  At special positions: 0
  Unit cell: (96.12, 114.48, 155.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      61     16.00
     O    2229      8.00
     N    2096      7.00
     C    7864      6.00
     H   12386      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 6.65
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 13 sheets defined
      50.5% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 82
      removed outlier: 3.709A  pdb=" N   GLU A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 91
      removed outlier: 3.751A  pdb=" N   LEU A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 94
      No H-bonds generated for 'chain 'A' and resid 92 through 94'
    Processing helix  chain 'A' and resid 115 through 118
    Processing helix  chain 'A' and resid 119 through 129
      removed outlier: 3.643A  pdb=" N   ARG A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 159
    Processing helix  chain 'A' and resid 171 through 180
    Processing helix  chain 'A' and resid 180 through 190
      removed outlier: 3.624A  pdb=" N   ARG A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 199
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 3.709A  pdb=" N   LYS A 213 " --> pdb=" O   GLU A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 253
    Processing helix  chain 'A' and resid 255 through 260
      removed outlier: 3.973A  pdb=" N   MET A 259 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 289
    Processing helix  chain 'A' and resid 290 through 299
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 335 through 340
    Processing helix  chain 'A' and resid 345 through 349
      removed outlier: 3.650A  pdb=" N   VAL A 349 " --> pdb=" O   HIS A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 357
      No H-bonds generated for 'chain 'A' and resid 355 through 357'
    Processing helix  chain 'A' and resid 421 through 423
      No H-bonds generated for 'chain 'A' and resid 421 through 423'
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 548 through 560
      removed outlier: 3.640A  pdb=" N   LYS A 553 " --> pdb=" O   ASN A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 578
    Processing helix  chain 'A' and resid 581 through 587
      Proline residue:  A 586  - end of helix
    Processing helix  chain 'A' and resid 588 through 593
    Processing helix  chain 'A' and resid 600 through 612
      removed outlier: 3.596A  pdb=" N   LEU A 610 " --> pdb=" O   LYS A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 620
    Processing helix  chain 'A' and resid 623 through 628
    Processing helix  chain 'A' and resid 637 through 649
      removed outlier: 3.541A  pdb=" N   ILE A 643 " --> pdb=" O   ASN A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 666
    Processing helix  chain 'A' and resid 667 through 670
    Processing helix  chain 'A' and resid 675 through 686
    Processing helix  chain 'A' and resid 690 through 706
      removed outlier: 3.974A  pdb=" N   PHE A 694 " --> pdb=" O   ARG A 690 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TRP A 697 " --> pdb=" O   HIS A 693 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLN A 705 " --> pdb=" O   SER A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 722
    Processing helix  chain 'A' and resid 726 through 752
      removed outlier: 3.553A  pdb=" N   PHE A 732 " --> pdb=" O   MET A 728 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL A 738 " --> pdb=" O   GLN A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 775
      removed outlier: 3.666A  pdb=" N   GLN A 775 " --> pdb=" O   LEU A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 838 through 858
      removed outlier: 3.669A  pdb=" N   GLU A 858 " --> pdb=" O   ILE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 888 through 894
    Processing helix  chain 'A' and resid 905 through 915
    Processing helix  chain 'A' and resid 917 through 943
    Processing helix  chain 'A' and resid 948 through 950
      No H-bonds generated for 'chain 'A' and resid 948 through 950'
    Processing helix  chain 'A' and resid 988 through 996
    Processing helix  chain 'A' and resid 1003 through 1022
    Processing helix  chain 'A' and resid 1023 through 1037
      removed outlier: 3.705A  pdb=" N   SER A1032 " --> pdb=" O   ILE A1028 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   MET A1033 " --> pdb=" O   ILE A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1055
      removed outlier: 3.564A  pdb=" N   ILE A1048 " --> pdb=" O   SER A1044 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   TYR A1050 " --> pdb=" O   GLU A1046 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   ILE A1051 " --> pdb=" O   ASP A1047 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ARG A1052 " --> pdb=" O   ILE A1048 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1060 through 1079
      removed outlier: 3.620A  pdb=" N   LYS A1078 " --> pdb=" O   VAL A1074 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLY A1079 " --> pdb=" O   CYS A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1092
      removed outlier: 3.726A  pdb=" N   ASN A1085 " --> pdb=" O   THR A1081 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 21
    Processing helix  chain 'B' and resid 38 through 48
      removed outlier: 4.737A  pdb=" N   TRP B  42 " --> pdb=" O   CYS B  38 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU B  44 " --> pdb=" O   ASN B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 52
      Proline residue:  B  52  - end of helix
      No H-bonds generated for 'chain 'B' and resid 49 through 52'
    Processing helix  chain 'B' and resid 53 through 73
      removed outlier: 4.094A  pdb=" N   ILE B  57 " --> pdb=" O   GLY B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 76
      No H-bonds generated for 'chain 'B' and resid 74 through 76'
    Processing helix  chain 'B' and resid 77 through 90
      removed outlier: 4.083A  pdb=" N   LEU B  81 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TYR B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU B  90 " --> pdb=" O   TYR B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 111
      removed outlier: 4.132A  pdb=" N   ARG B 111 " --> pdb=" O   ARG B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 115
    Processing helix  chain 'B' and resid 118 through 136
      removed outlier: 4.085A  pdb=" N   GLU B 125 " --> pdb=" O   SER B 121 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE B 129 " --> pdb=" O   GLU B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 150
      removed outlier: 3.728A  pdb=" N   LEU B 144 " --> pdb=" O   SER B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 184
    Processing helix  chain 'B' and resid 188 through 206
      removed outlier: 3.587A  pdb=" N   THR B 204 " --> pdb=" O   ALA B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 209
      No H-bonds generated for 'chain 'B' and resid 207 through 209'
    Processing helix  chain 'B' and resid 210 through 220
      removed outlier: 4.066A  pdb=" N   SER B 220 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 242
    Processing helix  chain 'B' and resid 245 through 265
      removed outlier: 3.704A  pdb=" N   ALA B 249 " --> pdb=" O   ASP B 245 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG B 250 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLN B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 270
      removed outlier: 3.628A  pdb=" N   LEU B 270 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 310
      removed outlier: 3.501A  pdb=" N   GLU B 303 " --> pdb=" O   ASP B 299 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU B 306 " --> pdb=" O   GLN B 302 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   LYS B 307 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU B 308 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU B 310 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 543
      removed outlier: 4.075A  pdb=" N   GLU B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 613
    Processing helix  chain 'B' and resid 613 through 620
    Processing helix  chain 'B' and resid 621 through 623
      No H-bonds generated for 'chain 'B' and resid 621 through 623'
    Processing helix  chain 'B' and resid 650 through 663
    Processing helix  chain 'B' and resid 696 through 702
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 61
      removed outlier: 3.850A  pdb=" N   GLY A 133 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   GLN A 134 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   GLN A 101 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 236
      removed outlier: 10.842A  pdb=" N   ILE A 303 " --> pdb=" O   CYS A 219 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   PHE A 221 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
      removed outlier: 8.336A  pdb=" N   LEU A 305 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   VAL A 223 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   LEU A 307 " --> pdb=" O   VAL A 223 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   HIS A 225 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353
      removed outlier: 6.392A  pdb=" N   VAL A 352 " --> pdb=" O   ALA A 528 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 419
      removed outlier: 7.519A  pdb=" N   VAL A 408 " --> pdb=" O   ASP A 369 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   ASP A 369 " --> pdb=" O   VAL A 408 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   TRP A 410 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLY A 367 " --> pdb=" O   TRP A 410 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   PHE A 361 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   SER A 517 " --> pdb=" O   ARG A 366 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ILE A 368 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   SER A 515 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398
    Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398
      removed outlier: 6.595A  pdb=" N   LEU A 429 " --> pdb=" O   ASN A 465 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ASN A 465 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LEU A 431 " --> pdb=" O   TYR A 463 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   TYR A 463 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE A 433 " --> pdb=" O   LEU A 461 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   TYR A 463 " --> pdb=" O   TRP A 485 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 783 through 784
      removed outlier: 5.349A  pdb=" N   LYS A 816 " --> pdb=" O   GLY A 794 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   LEU A 796 " --> pdb=" O   GLU A 814 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   GLU A 814 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS A 802 " --> pdb=" O   TRP A 812 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 783 through 784
      removed outlier: 5.349A  pdb=" N   LYS A 816 " --> pdb=" O   GLY A 794 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   LEU A 796 " --> pdb=" O   GLU A 814 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   GLU A 814 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 885 through 887
    Processing sheet with id=AB1, first strand: chain 'B' and resid 288 through 292
      removed outlier: 3.687A  pdb=" N   TYR B 291 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU B 166 " --> pdb=" O   TYR B 291 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL B 161 " --> pdb=" O   ARG B 516 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   VAL B 518 " --> pdb=" O   VAL B 161 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL B 163 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   PHE B 520 " --> pdb=" O   VAL B 163 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   LEU B 165 " --> pdb=" O   PHE B 520 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   SER B 513 " --> pdb=" O   LYS B 551 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   GLN B 553 " --> pdb=" O   SER B 513 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LEU B 515 " --> pdb=" O   GLN B 553 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   PHE B 555 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   VAL B 517 " --> pdb=" O   PHE B 555 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   VAL B 557 " --> pdb=" O   VAL B 517 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   VAL B 519 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 665 through 666
    Processing sheet with id=AB3, first strand: chain 'B' and resid 683 through 688
      removed outlier: 3.742A  pdb=" N   LYS B 732 " --> pdb=" O   ARG B 740 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 691 through 695
      removed outlier: 3.605A  pdb=" N   ASN B 752 " --> pdb=" O   ASN B 773 " (cutoff:3.500A)

    582 hydrogen bonds defined for protein.
    1650 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: 9.17

  Time building geometry restraints manager: 8.06 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 12350
        1.03 -     1.22: 36
        1.22 -     1.42: 5142
        1.42 -     1.61: 7286
        1.61 -     1.81: 86
  Bond restraints: 24900
  Sorted by residual:
  bond pdb=" N   THR B   7 "
       pdb=" CA  THR B   7 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  bond pdb=" N   LEU A  37 "
       pdb=" CA  LEU A  37 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.86e+00
  bond pdb=" N   THR B   7 "
       pdb=" H   THR B   7 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.36e+00
  bond pdb=" N   LEU A  37 "
       pdb=" H   LEU A  37 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.23e+00
  bond pdb=" NE2 GLN A 766 "
       pdb="HE22 GLN A 766 "
    ideal  model  delta    sigma   weight residual
    0.860  0.831  0.029 2.00e-02 2.50e+03 2.10e+00
  ... (remaining 24895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 44598
        1.71 -     3.42: 442
        3.42 -     5.14: 62
        5.14 -     6.85: 8
        6.85 -     8.56: 1
  Bond angle restraints: 45111
  Sorted by residual:
  angle pdb=" N   ILE A 387 "
        pdb=" CA  ILE A 387 "
        pdb=" C   ILE A 387 "
      ideal   model   delta    sigma   weight residual
     109.80  104.56    5.24 1.33e+00 5.65e-01 1.55e+01
  angle pdb=" N   ALA B 532 "
        pdb=" CA  ALA B 532 "
        pdb=" C   ALA B 532 "
      ideal   model   delta    sigma   weight residual
     111.36  107.15    4.21 1.09e+00 8.42e-01 1.49e+01
  angle pdb=" N   TYR B 533 "
        pdb=" CA  TYR B 533 "
        pdb=" C   TYR B 533 "
      ideal   model   delta    sigma   weight residual
     111.33  107.29    4.04 1.21e+00 6.83e-01 1.12e+01
  angle pdb=" N   LEU B 692 "
        pdb=" CA  LEU B 692 "
        pdb=" C   LEU B 692 "
      ideal   model   delta    sigma   weight residual
     107.20  112.34   -5.14 1.70e+00 3.46e-01 9.14e+00
  angle pdb=" N   ILE A1029 "
        pdb=" CA  ILE A1029 "
        pdb=" C   ILE A1029 "
      ideal   model   delta    sigma   weight residual
     113.39  109.10    4.29 1.47e+00 4.63e-01 8.52e+00
  ... (remaining 45106 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 10941
       17.95 -    35.90: 499
       35.90 -    53.86: 164
       53.86 -    71.81: 40
       71.81 -    89.76: 8
  Dihedral angle restraints: 11652
    sinusoidal: 6379
      harmonic: 5273
  Sorted by residual:
  dihedral pdb=" CA  PHE B 520 "
           pdb=" C   PHE B 520 "
           pdb=" N   GLY B 521 "
           pdb=" CA  GLY B 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.29  -27.71     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" N   LEU B  77 "
           pdb=" CA  LEU B  77 "
           pdb=" CB  LEU B  77 "
           pdb=" CG  LEU B  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.18  -59.82     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   ASN B 535 "
           pdb=" CA  ASN B 535 "
           pdb=" CB  ASN B 535 "
           pdb=" CG  ASN B 535 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.82   59.82     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 11649 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1395
       0.035 -    0.070: 387
       0.070 -    0.105: 109
       0.105 -    0.140: 44
       0.140 -    0.175: 4
  Chirality restraints: 1939
  Sorted by residual:
  chirality pdb=" CA  ILE B 122 "
            pdb=" N   ILE B 122 "
            pdb=" C   ILE B 122 "
            pdb=" CB  ILE B 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.62e-01
  chirality pdb=" CA  ILE B 729 "
            pdb=" N   ILE B 729 "
            pdb=" C   ILE B 729 "
            pdb=" CB  ILE B 729 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CA  VAL B 117 "
            pdb=" N   VAL B 117 "
            pdb=" C   VAL B 117 "
            pdb=" CB  VAL B 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.52e-01
  ... (remaining 1936 not shown)

  Planarity restraints: 3579
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 766 "    0.055 2.00e-02 2.50e+03   7.06e-02 7.47e+01
        pdb=" CD  GLN A 766 "   -0.039 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 766 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 766 "   -0.113 2.00e-02 2.50e+03
        pdb="HE21 GLN A 766 "   -0.010 2.00e-02 2.50e+03
        pdb="HE22 GLN A 766 "    0.111 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 130 "   -0.021 2.00e-02 2.50e+03   4.24e-02 1.79e+01
        pdb=" C   ILE B 130 "    0.073 2.00e-02 2.50e+03
        pdb=" O   ILE B 130 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ASP B 131 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 773 "   -0.026 2.00e-02 2.50e+03   3.34e-02 1.67e+01
        pdb=" CG  ASN A 773 "    0.017 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 773 "    0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 773 "    0.055 2.00e-02 2.50e+03
        pdb="HD21 ASN A 773 "    0.003 2.00e-02 2.50e+03
        pdb="HD22 ASN A 773 "   -0.052 2.00e-02 2.50e+03
  ... (remaining 3576 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 615
        2.14 -     2.76: 47509
        2.76 -     3.37: 65327
        3.37 -     3.99: 84528
        3.99 -     4.60: 135938
  Nonbonded interactions: 333917
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  66 "
            pdb=" H   GLN A  69 "
     model   vdw
     1.531 2.450
  nonbonded pdb="HE22 GLN A 114 "
            pdb=" O   CYS A 329 "
     model   vdw
     1.550 2.450
  nonbonded pdb=" H   THR B 222 "
            pdb=" OE2 GLU B 225 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" H   SER B 691 "
            pdb=" OD1 ASP B 817 "
     model   vdw
     1.604 2.450
  nonbonded pdb="HH22 ARG A 947 "
            pdb=" O   ASP A 964 "
     model   vdw
     1.608 2.450
  ... (remaining 333912 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:             1.900
  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:             0.390
  Extract box with map and model:          0.930
  Check model and map are aligned:         0.170
  Set scattering table:                    0.210
  Process input model:                     52.210
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
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      :  0.004   0.037  12514  Z= 0.185
  Angle     :  0.595   6.486  16955  Z= 0.335
  Chirality :  0.039   0.175   1939
  Planarity :  0.005   0.052   2141
  Dihedral  : 12.344  89.759   4648
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.63 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  :  6.98 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.21), residues: 1491
  helix: -0.54 (0.21), residues: 651
  sheet: -1.34 (0.31), residues: 230
  loop : -1.69 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 292 
 HIS   0.004   0.001   HIS A 693 
 PHE   0.021   0.001   PHE A 175 
 TYR   0.026   0.002   TYR B 533 
 ARG   0.003   0.000   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15368 (  577)
  hydrogen bonds       : angle       6.67212 ( 1650)
  covalent geometry    : bond        0.00387 (12514)
  covalent geometry    : angle       0.59517 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 249
  time to evaluate  : 2.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 HIS cc_start: 0.7874 (m90) cc_final: 0.7548 (m170)
REVERT: A  134 GLN cc_start: 0.7224 (mt0) cc_final: 0.6708 (mt0)
REVERT: A  209 GLU cc_start: 0.8061 (tt0) cc_final: 0.7506 (tp30)
REVERT: A  216 THR cc_start: 0.6959 (m) cc_final: 0.6739 (t)
REVERT: A  317 GLU cc_start: 0.7829 (pt0) cc_final: 0.7611 (pt0)
REVERT: A  320 LYS cc_start: 0.8219 (tttp) cc_final: 0.7991 (ttpt)
REVERT: A  479 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6815 (mt-10)
REVERT: A  497 PHE cc_start: 0.6306 (t80) cc_final: 0.5889 (t80)
REVERT: A  511 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6991 (tp30)
REVERT: A  531 LYS cc_start: 0.6769 (tttt) cc_final: 0.6321 (ttpp)
REVERT: A  646 GLN cc_start: 0.6253 (tt0) cc_final: 0.5805 (mt0)
REVERT: A  781 GLN cc_start: 0.7942 (mt0) cc_final: 0.7152 (mm110)
REVERT: A  804 MET cc_start: 0.7460 (mtp) cc_final: 0.7063 (mtp)
REVERT: A  809 LYS cc_start: 0.7272 (mttt) cc_final: 0.6425 (mmtt)
REVERT: A  883 LYS cc_start: 0.7656 (mttt) cc_final: 0.7003 (mmtm)
REVERT: A  953 MET cc_start: 0.6797 (mtp) cc_final: 0.6592 (mtp)
REVERT: A  982 ARG cc_start: 0.6948 (mtp180) cc_final: 0.6175 (mtt-85)
REVERT: A  995 MET cc_start: 0.5107 (mtt) cc_final: 0.4897 (mtt)
REVERT: A 1053 ASP cc_start: 0.6342 (m-30) cc_final: 0.6084 (m-30)
REVERT: A 1066 LYS cc_start: 0.6151 (tttp) cc_final: 0.5719 (mmmt)
REVERT: B   77 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7888 (tt)
REVERT: B   83 LEU cc_start: 0.7477 (mt) cc_final: 0.7233 (tt)
REVERT: B  216 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7755 (ttm110)
REVERT: B  217 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7550 (mmm-85)
REVERT: B  227 GLU cc_start: 0.7469 (tt0) cc_final: 0.7080 (tm-30)
REVERT: B  271 ASP cc_start: 0.7172 (t0) cc_final: 0.6859 (t0)
REVERT: B  279 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6883 (ttm170)
REVERT: B  537 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6678 (mmm160)
REVERT: B  548 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7768 (tpp-160)
REVERT: B  728 ILE cc_start: 0.7038 (mt) cc_final: 0.6752 (mt)
  outliers start: 38
  outliers final: 23
  residues processed: 283
  average time/residue: 0.7199
  time to fit residues: 273.5035
Evaluate side-chains
  198 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 173
  time to evaluate  : 1.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  724 CYS
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue   38 CYS
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  258 GLN
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  537 ARG
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  744 MET
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  771 THR
Chi-restraints excluded: chain B residue  793 SER
Chi-restraints excluded: chain B residue  815 CYS
Chi-restraints excluded: chain B residue  867 LEU
Chi-restraints excluded: chain B residue  873 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 127 optimal weight:    6.9990
   chunk 114 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 118 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 137 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  89 HIS
A 705 GLN
B 258 GLN
B 309 GLN
B 670 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.158053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.114290 restraints weight = 43694.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.40
r_work: 0.3174 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12514  Z= 0.137
  Angle     :  0.530   4.795  16955  Z= 0.275
  Chirality :  0.040   0.152   1939
  Planarity :  0.004   0.047   2141
  Dihedral  :  6.134  55.471   1674
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  9.92 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.21), residues: 1491
  helix:  0.45 (0.20), residues: 680
  sheet: -0.92 (0.32), residues: 234
  loop : -1.49 (0.24), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 812 
 HIS   0.004   0.001   HIS A 693 
 PHE   0.011   0.001   PHE B 230 
 TYR   0.009   0.001   TYR B 533 
 ARG   0.004   0.000   ARG B  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04927 (  577)
  hydrogen bonds       : angle       4.88202 ( 1650)
  covalent geometry    : bond        0.00305 (12514)
  covalent geometry    : angle       0.52950 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 174
  time to evaluate  : 1.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 HIS cc_start: 0.8664 (m90) cc_final: 0.8449 (m170)
REVERT: A  259 MET cc_start: 0.5165 (mmm) cc_final: 0.4958 (mmt)
REVERT: A  497 PHE cc_start: 0.7354 (t80) cc_final: 0.7131 (t80)
REVERT: A  777 LEU cc_start: 0.7260 (mt) cc_final: 0.7052 (mt)
REVERT: A  809 LYS cc_start: 0.8322 (mttt) cc_final: 0.7556 (mmtt)
REVERT: A  819 ASP cc_start: 0.8995 (t0) cc_final: 0.8676 (m-30)
REVERT: A  883 LYS cc_start: 0.8685 (mttt) cc_final: 0.8393 (mmtt)
REVERT: A  982 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7523 (mtt-85)
REVERT: A  995 MET cc_start: 0.8672 (mtt) cc_final: 0.7952 (mtt)
REVERT: A 1066 LYS cc_start: 0.8197 (tttp) cc_final: 0.7828 (mmmt)
REVERT: B  217 ARG cc_start: 0.8397 (mtt180) cc_final: 0.8010 (mmm-85)
  outliers start: 29
  outliers final: 19
  residues processed: 198
  average time/residue: 0.6722
  time to fit residues: 181.2768
Evaluate side-chains
  168 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 2.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 ASP
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue   22 HIS
Chi-restraints excluded: chain B residue   38 CYS
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  237 GLN
Chi-restraints excluded: chain B residue  258 GLN
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  679 ILE
Chi-restraints excluded: chain B residue  694 LEU
Chi-restraints excluded: chain B residue  744 MET
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  802 VAL
Chi-restraints excluded: chain B residue  867 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 71 optimal weight:    0.4980
   chunk 112 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 114 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 138 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 141 HIS
A 646 GLN
A 781 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.157023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.106430 restraints weight = 43752.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.49
r_work: 0.3169 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12514  Z= 0.121
  Angle     :  0.486   4.540  16955  Z= 0.250
  Chirality :  0.039   0.149   1939
  Planarity :  0.004   0.044   2141
  Dihedral  :  5.170  52.568   1656
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.46 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.22), residues: 1491
  helix:  1.03 (0.21), residues: 681
  sheet: -0.80 (0.33), residues: 233
  loop : -1.25 (0.24), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 812 
 HIS   0.005   0.001   HIS B 690 
 PHE   0.010   0.001   PHE A 961 
 TYR   0.010   0.001   TYR B 533 
 ARG   0.004   0.000   ARG B 543 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  577)
  hydrogen bonds       : angle       4.46702 ( 1650)
  covalent geometry    : bond        0.00279 (12514)
  covalent geometry    : angle       0.48576 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 1.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 MET cc_start: 0.5236 (mmm) cc_final: 0.5029 (mmt)
REVERT: A  777 LEU cc_start: 0.7227 (mt) cc_final: 0.7010 (mt)
REVERT: A  809 LYS cc_start: 0.8313 (mttt) cc_final: 0.7586 (mmtt)
REVERT: A  819 ASP cc_start: 0.9000 (t0) cc_final: 0.8697 (m-30)
REVERT: A  883 LYS cc_start: 0.8668 (mttt) cc_final: 0.8399 (mmtt)
REVERT: A  982 ARG cc_start: 0.7960 (mtp180) cc_final: 0.7538 (mtt-85)
REVERT: A  995 MET cc_start: 0.8667 (mtt) cc_final: 0.7904 (mtt)
REVERT: A 1066 LYS cc_start: 0.8209 (tttp) cc_final: 0.7847 (mmmt)
REVERT: B  217 ARG cc_start: 0.8429 (mtt180) cc_final: 0.7903 (mmm160)
REVERT: B  269 VAL cc_start: 0.7943 (t) cc_final: 0.7691 (t)
REVERT: B  270 LEU cc_start: 0.7887 (mp) cc_final: 0.7508 (mp)
REVERT: B  830 CYS cc_start: 0.7891 (t) cc_final: 0.7569 (t)
  outliers start: 16
  outliers final: 16
  residues processed: 169
  average time/residue: 0.6472
  time to fit residues: 153.6129
Evaluate side-chains
  162 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 1.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 HIS
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  237 GLN
Chi-restraints excluded: chain B residue  258 GLN
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  802 VAL
Chi-restraints excluded: chain B residue  867 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 116 optimal weight:    7.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    1.5986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.155518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.104832 restraints weight = 44050.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.50
r_work: 0.3129 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12514  Z= 0.181
  Angle     :  0.506   4.577  16955  Z= 0.263
  Chirality :  0.040   0.153   1939
  Planarity :  0.004   0.047   2141
  Dihedral  :  5.054  51.962   1650
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.39 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.22), residues: 1491
  helix:  1.09 (0.21), residues: 684
  sheet: -0.76 (0.33), residues: 236
  loop : -1.24 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 812 
 HIS   0.029   0.001   HIS A 141 
 PHE   0.013   0.002   PHE A 961 
 TYR   0.010   0.001   TYR B 141 
 ARG   0.002   0.000   ARG A 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04629 (  577)
  hydrogen bonds       : angle       4.40280 ( 1650)
  covalent geometry    : bond        0.00439 (12514)
  covalent geometry    : angle       0.50570 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 1.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.6756 (p-80)
REVERT: A  777 LEU cc_start: 0.7225 (mt) cc_final: 0.7005 (mt)
REVERT: A  809 LYS cc_start: 0.8333 (mttt) cc_final: 0.7600 (mmtt)
REVERT: A  819 ASP cc_start: 0.9012 (t0) cc_final: 0.8734 (m-30)
REVERT: A  883 LYS cc_start: 0.8707 (mttt) cc_final: 0.8410 (mmtt)
REVERT: A  982 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7611 (mtt-85)
REVERT: A  995 MET cc_start: 0.8668 (mtt) cc_final: 0.7923 (mtt)
REVERT: A 1066 LYS cc_start: 0.8257 (tttp) cc_final: 0.7892 (mmmt)
REVERT: B  217 ARG cc_start: 0.8443 (mtt180) cc_final: 0.8023 (mmm-85)
REVERT: B  269 VAL cc_start: 0.7905 (t) cc_final: 0.7678 (t)
REVERT: B  270 LEU cc_start: 0.7905 (mp) cc_final: 0.7542 (mp)
REVERT: B  678 PHE cc_start: 0.5885 (m-80) cc_final: 0.5520 (m-80)
REVERT: B  830 CYS cc_start: 0.7923 (t) cc_final: 0.7589 (t)
  outliers start: 22
  outliers final: 21
  residues processed: 171
  average time/residue: 0.6779
  time to fit residues: 162.3064
Evaluate side-chains
  169 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 2.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 HIS
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  769 GLN
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  967 HIS
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue   22 HIS
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  237 GLN
Chi-restraints excluded: chain B residue  258 GLN
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  802 VAL
Chi-restraints excluded: chain B residue  867 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 127 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 135 optimal weight:    7.9990
   chunk 128 optimal weight:    0.8980
   chunk 140 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 134 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 141 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.155008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.103594 restraints weight = 44140.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.53
r_work: 0.3126 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12514  Z= 0.156
  Angle     :  0.490   4.520  16955  Z= 0.254
  Chirality :  0.040   0.163   1939
  Planarity :  0.004   0.044   2141
  Dihedral  :  4.908  51.600   1649
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.83 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.22), residues: 1491
  helix:  1.22 (0.20), residues: 683
  sheet: -0.72 (0.33), residues: 236
  loop : -1.16 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 812 
 HIS   0.011   0.001   HIS A 141 
 PHE   0.012   0.001   PHE A 961 
 TYR   0.011   0.001   TYR B 291 
 ARG   0.005   0.000   ARG B 543 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04360 (  577)
  hydrogen bonds       : angle       4.28144 ( 1650)
  covalent geometry    : bond        0.00378 (12514)
  covalent geometry    : angle       0.48997 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 2.020 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  777 LEU cc_start: 0.7138 (mt) cc_final: 0.6920 (mt)
REVERT: A  809 LYS cc_start: 0.8328 (mttt) cc_final: 0.7571 (mmtt)
REVERT: A  819 ASP cc_start: 0.8998 (t0) cc_final: 0.8757 (m-30)
REVERT: A  883 LYS cc_start: 0.8714 (mttt) cc_final: 0.8479 (mmtt)
REVERT: A  982 ARG cc_start: 0.8077 (mtp180) cc_final: 0.7578 (mtt-85)
REVERT: A  995 MET cc_start: 0.8603 (mtt) cc_final: 0.8181 (mtt)
REVERT: A 1066 LYS cc_start: 0.8294 (tttp) cc_final: 0.7877 (mmmt)
REVERT: B  217 ARG cc_start: 0.8422 (mtt180) cc_final: 0.7977 (mmm-85)
REVERT: B  270 LEU cc_start: 0.7924 (mp) cc_final: 0.7578 (mp)
REVERT: B  678 PHE cc_start: 0.5747 (m-80) cc_final: 0.5372 (m-80)
REVERT: B  830 CYS cc_start: 0.7958 (t) cc_final: 0.7619 (t)
  outliers start: 24
  outliers final: 22
  residues processed: 172
  average time/residue: 0.6347
  time to fit residues: 152.7950
Evaluate side-chains
  168 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 1.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  141 HIS
Chi-restraints excluded: chain A residue  295 GLN
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  967 HIS
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue   22 HIS
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  237 GLN
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  802 VAL
Chi-restraints excluded: chain B residue  867 LEU
Chi-restraints excluded: chain B residue  869 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.154294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.103032 restraints weight = 43780.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.52
r_work: 0.3119 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12514  Z= 0.165
  Angle     :  0.496   4.527  16955  Z= 0.257
  Chirality :  0.040   0.147   1939
  Planarity :  0.004   0.044   2141
  Dihedral  :  4.660  51.254   1646
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.20 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.22), residues: 1491
  helix:  1.28 (0.20), residues: 683
  sheet: -0.74 (0.32), residues: 244
  loop : -1.14 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 812 
 HIS   0.021   0.001   HIS A 141 
 PHE   0.012   0.001   PHE A 961 
 TYR   0.010   0.001   TYR B 141 
 ARG   0.003   0.000   ARG A 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04372 (  577)
  hydrogen bonds       : angle       4.25247 ( 1650)
  covalent geometry    : bond        0.00402 (12514)
  covalent geometry    : angle       0.49556 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 2.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  777 LEU cc_start: 0.7130 (mt) cc_final: 0.6915 (mt)
REVERT: A  809 LYS cc_start: 0.8358 (mttt) cc_final: 0.7612 (mmtt)
REVERT: A  982 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7604 (mtt-85)
REVERT: A  995 MET cc_start: 0.8591 (mtt) cc_final: 0.8163 (mtt)
REVERT: A 1066 LYS cc_start: 0.8324 (tttp) cc_final: 0.7923 (mmmt)
REVERT: B  217 ARG cc_start: 0.8439 (mtt180) cc_final: 0.7976 (mmm-85)
REVERT: B  270 LEU cc_start: 0.7951 (mp) cc_final: 0.7674 (mp)
REVERT: B  696 HIS cc_start: 0.3134 (OUTLIER) cc_final: 0.2328 (t-90)
  outliers start: 25
  outliers final: 21
  residues processed: 170
  average time/residue: 0.6524
  time to fit residues: 153.7757
Evaluate side-chains
  161 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 2.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  295 GLN
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  769 GLN
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  967 HIS
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue   22 HIS
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  237 GLN
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  696 HIS
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  802 VAL
Chi-restraints excluded: chain B residue  869 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 46 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.155501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.104283 restraints weight = 43840.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.52
r_work: 0.3134 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12514  Z= 0.114
  Angle     :  0.468   4.469  16955  Z= 0.241
  Chirality :  0.039   0.150   1939
  Planarity :  0.003   0.041   2141
  Dihedral  :  4.380  50.913   1643
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.20 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.22), residues: 1491
  helix:  1.50 (0.20), residues: 683
  sheet: -0.63 (0.32), residues: 235
  loop : -1.02 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 812 
 HIS   0.011   0.001   HIS A 141 
 PHE   0.010   0.001   PHE A1068 
 TYR   0.010   0.001   TYR A 935 
 ARG   0.003   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  577)
  hydrogen bonds       : angle       4.12539 ( 1650)
  covalent geometry    : bond        0.00272 (12514)
  covalent geometry    : angle       0.46792 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 1.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  777 LEU cc_start: 0.7047 (mt) cc_final: 0.6844 (mt)
REVERT: A  809 LYS cc_start: 0.8329 (mttt) cc_final: 0.7574 (mmtt)
REVERT: A  819 ASP cc_start: 0.8978 (t0) cc_final: 0.8762 (m-30)
REVERT: A  982 ARG cc_start: 0.8048 (mtp180) cc_final: 0.7601 (mtt-85)
REVERT: A  995 MET cc_start: 0.8583 (mtt) cc_final: 0.8164 (mtt)
REVERT: A 1066 LYS cc_start: 0.8335 (tttp) cc_final: 0.7961 (mmmt)
REVERT: B  217 ARG cc_start: 0.8437 (mtt180) cc_final: 0.7948 (mmm-85)
REVERT: B  270 LEU cc_start: 0.7948 (mp) cc_final: 0.7708 (mp)
REVERT: B  696 HIS cc_start: 0.3256 (OUTLIER) cc_final: 0.2413 (t-90)
  outliers start: 20
  outliers final: 16
  residues processed: 157
  average time/residue: 0.6446
  time to fit residues: 141.0333
Evaluate side-chains
  154 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 1.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  967 HIS
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  237 GLN
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  696 HIS
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  802 VAL
Chi-restraints excluded: chain B residue  869 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 146 optimal weight:    0.0980
   chunk 135 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.156375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.113360 restraints weight = 42829.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.23
r_work: 0.3152 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12514  Z= 0.098
  Angle     :  0.451   4.469  16955  Z= 0.231
  Chirality :  0.039   0.151   1939
  Planarity :  0.003   0.039   2141
  Dihedral  :  4.224  50.304   1643
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.71 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.22), residues: 1491
  helix:  1.76 (0.20), residues: 688
  sheet: -0.58 (0.32), residues: 235
  loop : -0.96 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 812 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.010   0.001   PHE A1068 
 TYR   0.010   0.001   TYR B 730 
 ARG   0.003   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  577)
  hydrogen bonds       : angle       3.99397 ( 1650)
  covalent geometry    : bond        0.00233 (12514)
  covalent geometry    : angle       0.45084 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 2.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  777 LEU cc_start: 0.7057 (mt) cc_final: 0.6836 (mt)
REVERT: A  809 LYS cc_start: 0.8317 (mttt) cc_final: 0.7574 (mmtt)
REVERT: A  819 ASP cc_start: 0.8966 (t0) cc_final: 0.8748 (m-30)
REVERT: A  982 ARG cc_start: 0.8023 (mtp180) cc_final: 0.7610 (mtt-85)
REVERT: A  995 MET cc_start: 0.8529 (mtt) cc_final: 0.7762 (mtt)
REVERT: A 1066 LYS cc_start: 0.8290 (tttp) cc_final: 0.7941 (mmmt)
REVERT: B  217 ARG cc_start: 0.8421 (mtt180) cc_final: 0.7807 (mmm160)
REVERT: B  270 LEU cc_start: 0.8063 (mp) cc_final: 0.7842 (mp)
REVERT: B  696 HIS cc_start: 0.3227 (OUTLIER) cc_final: 0.2263 (t-90)
REVERT: B  752 ASN cc_start: 0.6016 (m-40) cc_final: 0.5502 (m-40)
  outliers start: 16
  outliers final: 13
  residues processed: 155
  average time/residue: 0.6283
  time to fit residues: 137.3585
Evaluate side-chains
  150 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 2.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLN
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  967 HIS
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  696 HIS
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  802 VAL
Chi-restraints excluded: chain B residue  869 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 113 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 133 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.156316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.105066 restraints weight = 44021.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.53
r_work: 0.3144 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12514  Z= 0.109
  Angle     :  0.458   4.459  16955  Z= 0.233
  Chirality :  0.039   0.150   1939
  Planarity :  0.003   0.041   2141
  Dihedral  :  4.130  49.646   1641
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.86 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.22), residues: 1491
  helix:  1.89 (0.20), residues: 688
  sheet: -0.52 (0.32), residues: 235
  loop : -0.95 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 812 
 HIS   0.003   0.001   HIS A 225 
 PHE   0.010   0.001   PHE A1068 
 TYR   0.009   0.001   TYR B 730 
 ARG   0.003   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03687 (  577)
  hydrogen bonds       : angle       3.97075 ( 1650)
  covalent geometry    : bond        0.00262 (12514)
  covalent geometry    : angle       0.45793 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 2.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  777 LEU cc_start: 0.7111 (mt) cc_final: 0.6878 (mt)
REVERT: A  819 ASP cc_start: 0.8953 (t0) cc_final: 0.8744 (m-30)
REVERT: A  982 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7604 (mtt-85)
REVERT: A  995 MET cc_start: 0.8548 (mtt) cc_final: 0.7750 (mtt)
REVERT: A 1066 LYS cc_start: 0.8308 (tttp) cc_final: 0.7946 (mmmt)
REVERT: B  217 ARG cc_start: 0.8418 (mtt180) cc_final: 0.7801 (mmm160)
REVERT: B  692 LEU cc_start: 0.7304 (tt) cc_final: 0.6917 (tp)
REVERT: B  696 HIS cc_start: 0.3176 (OUTLIER) cc_final: 0.2247 (t-90)
  outliers start: 15
  outliers final: 13
  residues processed: 154
  average time/residue: 0.6345
  time to fit residues: 139.0847
Evaluate side-chains
  151 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 1.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLN
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  967 HIS
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  696 HIS
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  802 VAL
Chi-restraints excluded: chain B residue  869 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 135 optimal weight:    6.9990
   chunk 102 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.155732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.106873 restraints weight = 43128.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.04
r_work: 0.3165 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12514  Z= 0.122
  Angle     :  0.464   4.773  16955  Z= 0.238
  Chirality :  0.039   0.149   1939
  Planarity :  0.004   0.062   2141
  Dihedral  :  4.133  48.961   1641
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 13.08 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.22), residues: 1491
  helix:  1.91 (0.20), residues: 688
  sheet: -0.55 (0.31), residues: 247
  loop : -0.93 (0.25), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 812 
 HIS   0.003   0.001   HIS A 225 
 PHE   0.010   0.001   PHE A 961 
 TYR   0.009   0.001   TYR B 730 
 ARG   0.003   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03760 (  577)
  hydrogen bonds       : angle       3.98455 ( 1650)
  covalent geometry    : bond        0.00295 (12514)
  covalent geometry    : angle       0.46436 (16955)

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

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

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2982 Ramachandran restraints generated.
    1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 2.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  777 LEU cc_start: 0.7103 (mt) cc_final: 0.6867 (mt)
REVERT: A  982 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7615 (mtt-85)
REVERT: A  995 MET cc_start: 0.8471 (mtt) cc_final: 0.7696 (mtt)
REVERT: A 1066 LYS cc_start: 0.8275 (tttp) cc_final: 0.7938 (mmmt)
REVERT: B  217 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7778 (mmm160)
REVERT: B  692 LEU cc_start: 0.7571 (tt) cc_final: 0.6923 (tp)
REVERT: B  693 GLU cc_start: 0.5098 (tt0) cc_final: 0.4889 (tt0)
  outliers start: 14
  outliers final: 14
  residues processed: 151
  average time/residue: 0.6117
  time to fit residues: 129.6903
Evaluate side-chains
  149 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 1.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLN
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  967 HIS
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  156 HIS
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  802 VAL
Chi-restraints excluded: chain B residue  869 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0870
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 139 optimal weight:    0.0370
   chunk 44 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7838

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.156354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.112500 restraints weight = 43299.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.24
r_work: 0.3145 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12514  Z= 0.109
  Angle     :  0.459   4.579  16955  Z= 0.234
  Chirality :  0.039   0.151   1939
  Planarity :  0.003   0.051   2141
  Dihedral  :  4.072  48.165   1641
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.67 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.22), residues: 1491
  helix:  1.98 (0.20), residues: 689
  sheet: -0.51 (0.31), residues: 248
  loop : -0.89 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 812 
 HIS   0.003   0.001   HIS A 708 
 PHE   0.010   0.001   PHE A1068 
 TYR   0.010   0.001   TYR B 730 
 ARG   0.004   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  577)
  hydrogen bonds       : angle       3.94729 ( 1650)
  covalent geometry    : bond        0.00261 (12514)
  covalent geometry    : angle       0.45861 (16955)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14589.33 seconds
wall clock time: 247 minutes 25.73 seconds (14845.73 seconds total)