Starting phenix.real_space_refine
on Thu Sep 18 05:58:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fux_50781/09_2025/9fux_50781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fux_50781/09_2025/9fux_50781.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fux_50781/09_2025/9fux_50781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fux_50781/09_2025/9fux_50781.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fux_50781/09_2025/9fux_50781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fux_50781/09_2025/9fux_50781.map"
  }
  resolution = 2.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.908
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
     Zn      2      6.06       5
     S      95      5.16       5
     C    9239      2.51       5
     N    2472      2.21       5
     O    2748      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14556
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 10357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1286, 10357
          Classifications: {'peptide': 1286}
          Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1235}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 927
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 116, 919
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
      Conformer: "B"
        Number of residues, atoms: 116, 919
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
          bond proxies already assigned to first conformer: 924
    Chain: "D"
      Number of atoms: 861
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 861
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "E"
      Number of atoms: 1591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1591
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 7, 'TRANS': 190}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 818
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 4, 'TRANS': 98}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8874  SG  CYS A1236      74.668  72.251  38.143  1.00 30.25           S
  ATOM   8897  SG  CYS A1239      74.485  75.323  40.610  1.00 34.30           S
  ATOM   8524  SG  CYS A1191      55.646  77.046  29.002  1.00 21.90           S
  ATOM  10084  SG  CYS A1428      59.856  76.179  28.728  1.00 48.19           S
  ATOM  10090  SG  CYS A1429      57.696  75.232  31.337  1.00 32.05           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASN C 486 " occ=0.26
      ... (14 atoms not shown)
      pdb=" ND2BASN C 486 " occ=0.74
  Time building chain proxies: 2.84, per 1000 atoms: 0.20
  Number of scatterers: 14556
  At special positions: 0
  Unit cell: (93.4784, 102.242, 191.339, 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)
     Zn      2     29.99
     S      95     16.00
     O    2748      8.00
     N    2472      7.00
     C    9239      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 512 " - pdb=" SG  CYS F 512 " distance=2.03

  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: 0.90
  Conformation dependent library (CDL) restraints added in 541.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2301 "
        pdb="ZN    ZN A2301 " - pdb=" NE2 HIS A1423 "
        pdb="ZN    ZN A2301 " - pdb=" ND1 HIS A1421 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A1236 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A1239 "
      pdb="  ZN A2302 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A1428 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A1191 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A1429 "
      Number of angles added : 1


  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3466

  Finding SS restraints...
    Secondary structure from input PDB file:
      86 helices and 10 sheets defined
      63.2% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 11
      removed outlier: 3.874A  pdb=" N   ILE A  11 " --> pdb=" O   SER A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 34
    Processing helix  chain 'A' and resid 43 through 56
    Processing helix  chain 'A' and resid 60 through 77
    Processing helix  chain 'A' and resid 104 through 137
      removed outlier: 3.680A  pdb=" N   ILE A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   LYS A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   LYS A 124 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 156
      removed outlier: 3.560A  pdb=" N   GLU A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ILE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 146 " --> pdb=" O   ARG A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 166 through 188
      removed outlier: 3.553A  pdb=" N   GLN A 188 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 194
      removed outlier: 3.542A  pdb=" N   ARG A 193 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   SER A 194 " --> pdb=" O   LYS A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 255
    Processing helix  chain 'A' and resid 256 through 259
    Processing helix  chain 'A' and resid 260 through 273
      removed outlier: 3.829A  pdb=" N   ARG A 264 " --> pdb=" O   PRO A 260 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ASN A 266 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 280
      removed outlier: 4.398A  pdb=" N   VAL A 278 " --> pdb=" O   PRO A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 288
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 304 through 308
    Processing helix  chain 'A' and resid 309 through 325
      removed outlier: 3.897A  pdb=" N   HIS A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 346
    Processing helix  chain 'A' and resid 349 through 355
    Processing helix  chain 'A' and resid 356 through 360
      removed outlier: 3.609A  pdb=" N   PHE A 359 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   PHE A 360 " --> pdb=" O   PHE A 357 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 356 through 360'
    Processing helix  chain 'A' and resid 369 through 378
    Processing helix  chain 'A' and resid 389 through 410
      removed outlier: 3.747A  pdb=" N   ARG A 410 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 435
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 447 through 451
    Processing helix  chain 'A' and resid 479 through 487
      removed outlier: 3.575A  pdb=" N   TRP A 483 " --> pdb=" O   LYS A 480 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   ASP A 484 " --> pdb=" O   ASP A 481 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   VAL A 486 " --> pdb=" O   TRP A 483 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR A 487 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
    Processing helix  chain 'A' and resid 504 through 511
      removed outlier: 3.519A  pdb=" N   ASN A 511 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 526
      removed outlier: 3.617A  pdb=" N   TYR A 523 " --> pdb=" O   ASN A 519 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   VAL A 524 " --> pdb=" O   MET A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 574
    Processing helix  chain 'A' and resid 575 through 578
    Processing helix  chain 'A' and resid 725 through 730
    Processing helix  chain 'A' and resid 731 through 746
      removed outlier: 4.858A  pdb=" N   ILE A 737 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   PHE A 738 " --> pdb=" O   SER A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 761
    Processing helix  chain 'A' and resid 802 through 822
      Proline residue:  A 812  - end of helix
    Processing helix  chain 'A' and resid 847 through 874
    Processing helix  chain 'A' and resid 904 through 910
      removed outlier: 3.728A  pdb=" N   SER A 908 " --> pdb=" O   GLN A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 940
    Processing helix  chain 'A' and resid 943 through 965
    Processing helix  chain 'A' and resid 972 through 982
      Proline residue:  A 978  - end of helix
      removed outlier: 3.546A  pdb=" N   ASN A 982 " --> pdb=" O   PRO A 978 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 992
    Processing helix  chain 'A' and resid 993 through 997
    Processing helix  chain 'A' and resid 1014 through 1029
    Processing helix  chain 'A' and resid 1033 through 1041
      removed outlier: 3.688A  pdb=" N   LEU A1037 " --> pdb=" O   THR A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1056
    Processing helix  chain 'A' and resid 1067 through 1083
      removed outlier: 3.610A  pdb=" N   ILE A1080 " --> pdb=" O   THR A1076 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASN A1083 " --> pdb=" O   THR A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1110
    Processing helix  chain 'A' and resid 1115 through 1126
    Processing helix  chain 'A' and resid 1126 through 1138
    Processing helix  chain 'A' and resid 1155 through 1164
      removed outlier: 3.771A  pdb=" N   VAL A1159 " --> pdb=" O   GLN A1155 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   SER A1160 " --> pdb=" O   PRO A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1178
    Processing helix  chain 'A' and resid 1191 through 1204
    Processing helix  chain 'A' and resid 1204 through 1209
    Processing helix  chain 'A' and resid 1220 through 1224
    Processing helix  chain 'A' and resid 1236 through 1242
    Processing helix  chain 'A' and resid 1291 through 1309
    Processing helix  chain 'A' and resid 1311 through 1323
    Processing helix  chain 'A' and resid 1329 through 1337
    Processing helix  chain 'A' and resid 1366 through 1370
    Processing helix  chain 'A' and resid 1393 through 1398
    Processing helix  chain 'A' and resid 1400 through 1407
    Processing helix  chain 'C' and resid 482 through 486
      removed outlier: 3.615A  pdb=" N  AASN C 486 " --> pdb=" O   ASP C 483 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 489 through 501
    Processing helix  chain 'C' and resid 502 through 506
      removed outlier: 3.663A  pdb=" N   ASP C 505 " --> pdb=" O   HIS C 502 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   TYR C 506 " --> pdb=" O   LEU C 503 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 502 through 506'
    Processing helix  chain 'C' and resid 507 through 541
      removed outlier: 4.119A  pdb=" N   GLY C 519 " --> pdb=" O   SER C 515 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLN C 539 " --> pdb=" O   HIS C 535 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 542 through 578
      removed outlier: 3.709A  pdb=" N   ILE C 547 " --> pdb=" O   ILE C 543 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASN C 548 " --> pdb=" O   PRO C 544 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 590 through 594
    Processing helix  chain 'D' and resid 479 through 485
    Processing helix  chain 'D' and resid 489 through 502
      removed outlier: 3.547A  pdb=" N   HIS D 499 " --> pdb=" O   ARG D 495 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   HIS D 502 " --> pdb=" O   TYR D 498 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 503 through 506
      removed outlier: 3.617A  pdb=" N   TYR D 506 " --> pdb=" O   LEU D 503 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 503 through 506'
    Processing helix  chain 'D' and resid 507 through 538
      removed outlier: 3.535A  pdb=" N   ILE D 521 " --> pdb=" O   LEU D 517 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU D 538 " --> pdb=" O   ASN D 534 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 539 through 541
      No H-bonds generated for 'chain 'D' and resid 539 through 541'
    Processing helix  chain 'D' and resid 542 through 573
      removed outlier: 3.681A  pdb=" N   SER D 573 " --> pdb=" O   GLY D 569 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 489 through 501
    Processing helix  chain 'E' and resid 502 through 506
      removed outlier: 3.539A  pdb=" N   ASP E 505 " --> pdb=" O   HIS E 502 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   TYR E 506 " --> pdb=" O   LEU E 503 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 502 through 506'
    Processing helix  chain 'E' and resid 507 through 540
      removed outlier: 3.575A  pdb=" N   VAL E 516 " --> pdb=" O   CYS E 512 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU E 517 " --> pdb=" O   GLU E 513 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 542 through 573
      removed outlier: 3.704A  pdb=" N   ASN E 548 " --> pdb=" O   PRO E 544 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS E 549 " --> pdb=" O   LYS E 545 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 602 through 607
      removed outlier: 3.695A  pdb=" N   SER E 607 " --> pdb=" O   GLU E 604 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 635 through 638
      removed outlier: 3.648A  pdb=" N   ILE E 638 " --> pdb=" O   GLU E 635 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 635 through 638'
    Processing helix  chain 'E' and resid 657 through 672
    Processing helix  chain 'E' and resid 676 through 687
    Processing helix  chain 'E' and resid 690 through 706
      removed outlier: 3.527A  pdb=" N   ASN E 699 " --> pdb=" O   GLN E 695 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 479 through 484
    Processing helix  chain 'F' and resid 489 through 504
      removed outlier: 3.595A  pdb=" N   ARG F 495 " --> pdb=" O   HIS F 491 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   HIS F 499 " --> pdb=" O   ARG F 495 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   HIS F 502 " --> pdb=" O   TYR F 498 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLY F 504 " --> pdb=" O   ALA F 500 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 507 through 541
      removed outlier: 3.505A  pdb=" N   SER F 515 " --> pdb=" O   LEU F 511 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   VAL F 516 " --> pdb=" O   CYS F 512 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL F 520 " --> pdb=" O   VAL F 516 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE F 521 " --> pdb=" O   LEU F 517 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLN F 539 " --> pdb=" O   HIS F 535 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LYS F 541 " --> pdb=" O   GLU F 537 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 542 through 574
      removed outlier: 3.671A  pdb=" N   SER F 573 " --> pdb=" O   GLY F 569 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   MET F 574 " --> pdb=" O   HIS F 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22
      removed outlier: 6.895A  pdb=" N   ILE A  21 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388
    Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 419
    Processing sheet with id=AA5, first strand: chain 'A' and resid 553 through 556
      removed outlier: 7.269A  pdb=" N   VAL A 537 " --> pdb=" O   TYR A 765 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ALA A 767 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   TYR A 539 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 824 through 827
      removed outlier: 3.934A  pdb=" N   ARG A 824 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ALA A 837 " --> pdb=" O   ALA A 826 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 891
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1113 through 1114
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1225 through 1230
    Processing sheet with id=AB1, first strand: chain 'E' and resid 609 through 610

    823 hydrogen bonds defined for protein.
    2355 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4777
        1.34 -     1.46: 2375
        1.46 -     1.58: 7520
        1.58 -     1.70: 0
        1.70 -     1.82: 158
  Bond restraints: 14830
  Sorted by residual:
  bond pdb=" CG  LEU A 242 "
       pdb=" CD1 LEU A 242 "
    ideal  model  delta    sigma   weight residual
    1.521  1.438  0.083 3.30e-02 9.18e+02 6.29e+00
  bond pdb=" C   VAL E 653 "
       pdb=" N   PRO E 654 "
    ideal  model  delta    sigma   weight residual
    1.335  1.322  0.013 8.70e-03 1.32e+04 2.25e+00
  bond pdb=" CB  ARG A 561 "
       pdb=" CG  ARG A 561 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.11e+00
  bond pdb=" CB  ARG A 408 "
       pdb=" CG  ARG A 408 "
    ideal  model  delta    sigma   weight residual
    1.520  1.479  0.041 3.00e-02 1.11e+03 1.91e+00
  bond pdb=" C   GLY A1060 "
       pdb=" O   GLY A1060 "
    ideal  model  delta    sigma   weight residual
    1.239  1.229  0.010 7.10e-03 1.98e+04 1.83e+00
  ... (remaining 14825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.89: 19865
        2.89 -     5.78: 167
        5.78 -     8.67: 6
        8.67 -    11.56: 2
       11.56 -    14.45: 3
  Bond angle restraints: 20043
  Sorted by residual:
  angle pdb=" CA  LEU A 242 "
        pdb=" CB  LEU A 242 "
        pdb=" CG  LEU A 242 "
      ideal   model   delta    sigma   weight residual
     116.30  101.85   14.45 3.50e+00 8.16e-02 1.70e+01
  angle pdb=" N   VAL A1366 "
        pdb=" CA  VAL A1366 "
        pdb=" C   VAL A1366 "
      ideal   model   delta    sigma   weight residual
     113.42  109.08    4.34 1.17e+00 7.31e-01 1.38e+01
  angle pdb=" CA  LEU A 210 "
        pdb=" CB  LEU A 210 "
        pdb=" CG  LEU A 210 "
      ideal   model   delta    sigma   weight residual
     116.30  128.81  -12.51 3.50e+00 8.16e-02 1.28e+01
  angle pdb=" CA  LEU A1138 "
        pdb=" CB  LEU A1138 "
        pdb=" CG  LEU A1138 "
      ideal   model   delta    sigma   weight residual
     116.30  128.11  -11.81 3.50e+00 8.16e-02 1.14e+01
  angle pdb=" CG1 ILE A1145 "
        pdb=" CB  ILE A1145 "
        pdb=" CG2 ILE A1145 "
      ideal   model   delta    sigma   weight residual
     110.70  100.59   10.11 3.00e+00 1.11e-01 1.14e+01
  ... (remaining 20038 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 8135
       17.31 -    34.62: 789
       34.62 -    51.94: 115
       51.94 -    69.25: 33
       69.25 -    86.56: 10
  Dihedral angle restraints: 9082
    sinusoidal: 3753
      harmonic: 5329
  Sorted by residual:
  dihedral pdb=" CA  LEU A 919 "
           pdb=" C   LEU A 919 "
           pdb=" N   VAL A 920 "
           pdb=" CA  VAL A 920 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.65   25.35     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  PHE A1379 "
           pdb=" C   PHE A1379 "
           pdb=" N   ARG A1380 "
           pdb=" CA  ARG A1380 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.15   20.85     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  MET A 755 "
           pdb=" C   MET A 755 "
           pdb=" N   HIS A 756 "
           pdb=" CA  HIS A 756 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.30   20.70     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 9079 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1794
       0.056 -    0.112: 437
       0.112 -    0.167: 44
       0.167 -    0.223: 1
       0.223 -    0.279: 1
  Chirality restraints: 2277
  Sorted by residual:
  chirality pdb=" CB  ILE A1145 "
            pdb=" CA  ILE A1145 "
            pdb=" CG1 ILE A1145 "
            pdb=" CG2 ILE A1145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.92   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CB  ILE A 367 "
            pdb=" CA  ILE A 367 "
            pdb=" CG1 ILE A 367 "
            pdb=" CG2 ILE A 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  VAL A1218 "
            pdb=" N   VAL A1218 "
            pdb=" C   VAL A1218 "
            pdb=" CB  VAL A1218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.29e-01
  ... (remaining 2274 not shown)

  Planarity restraints: 2565
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 529 "    0.031 2.00e-02 2.50e+03   2.56e-02 1.32e+01
        pdb=" CG  TYR A 529 "   -0.062 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 529 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 529 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 529 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 529 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 529 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 529 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1379 "   -0.019 2.00e-02 2.50e+03   1.92e-02 6.47e+00
        pdb=" CG  PHE A1379 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1379 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1379 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1379 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1379 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1379 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 911 "   -0.216 9.50e-02 1.11e+02   9.68e-02 5.97e+00
        pdb=" NE  ARG A 911 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 911 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 911 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 911 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2562 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 95
        2.57 -     3.16: 11716
        3.16 -     3.74: 23247
        3.74 -     4.32: 33900
        4.32 -     4.90: 54426
  Nonbonded interactions: 123384
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 916 "
            pdb=" OD1 ASN A 929 "
     model   vdw
     1.993 3.040
  nonbonded pdb=" OH  TYR A 897 "
            pdb=" OE1 GLN A1259 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OG1 THR A 972 "
            pdb=" OD1 ASP A 974 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   ILE A1072 "
            pdb=" OG1 THR A1076 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" NE2 GLN A 139 "
            pdb=" OD2 ASP A 143 "
     model   vdw
     2.189 3.120
  ... (remaining 123379 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 480 through 485 or resid 487 through 580))
  selection = (chain 'D' and (resid 480 through 485 or resid 487 through 580))
  selection = (chain 'F' and (resid 480 through 485 or resid 487 through 580))
}

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=0.26 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:             11.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     13.950
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
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      :  0.006   0.083  14838  Z= 0.235
  Angle     :  0.701  14.447  20046  Z= 0.364
  Chirality :  0.046   0.279   2277
  Planarity :  0.006   0.098   2565
  Dihedral  : 13.846  86.562   5613
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.69 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.20), residues: 1792
  helix:  0.64 (0.16), residues: 1041
  sheet:  0.34 (0.53), residues: 92
  loop : -0.56 (0.24), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 911 
 TYR   0.062   0.003   TYR A 529 
 PHE   0.044   0.002   PHE A1379 
 TRP   0.023   0.003   TRP A 754 
 HIS   0.007   0.001   HIS D 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 (14830)
  covalent geometry    : angle       0.70092 (20043)
  SS BOND              : bond        0.00126 (    1)
  SS BOND              : angle       0.91147 (    2)
  hydrogen bonds       : bond        0.18932 (  823)
  hydrogen bonds       : angle       6.30269 ( 2355)
  metal coordination   : bond        0.00700 (    7)
  metal coordination   : angle       1.61346 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  503 ARG cc_start: 0.6400 (ttm110) cc_final: 0.6013 (pmm150)
REVERT: A 1075 ILE cc_start: 0.7937 (mp) cc_final: 0.7721 (mp)
REVERT: C  531 MET cc_start: 0.7274 (mmt) cc_final: 0.6773 (mpt)
REVERT: D  531 MET cc_start: 0.6135 (mtt) cc_final: 0.5900 (OUTLIER)
  outliers start: 0
  outliers final: 1
  residues processed: 239
  average time/residue: 0.7054
  time to fit residues: 182.3867
Evaluate side-chains
  201 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 858 GLN
A1094 HIS
A1374 ASN
A1394 GLN
A1438 GLN
E 632 GLN
** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 535 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.194761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.142715 restraints weight = 16396.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 2.36
r_work: 0.3560 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14838  Z= 0.147
  Angle     :  0.601  12.714  20046  Z= 0.311
  Chirality :  0.042   0.202   2277
  Planarity :  0.004   0.054   2565
  Dihedral  :  4.710  25.128   1951
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.19 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.66 %
    Favored  : 91.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.20), residues: 1792
  helix:  1.31 (0.16), residues: 1049
  sheet:  0.90 (0.53), residues: 83
  loop : -0.43 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1295 
 TYR   0.022   0.002   TYR A 529 
 PHE   0.026   0.001   PHE A1379 
 TRP   0.015   0.002   TRP A 754 
 HIS   0.006   0.001   HIS D 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (14830)
  covalent geometry    : angle       0.60111 (20043)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       1.27690 (    2)
  hydrogen bonds       : bond        0.05417 (  823)
  hydrogen bonds       : angle       4.62375 ( 2355)
  metal coordination   : bond        0.00336 (    7)
  metal coordination   : angle       1.28076 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 220
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
REVERT: A  503 ARG cc_start: 0.6942 (ttm110) cc_final: 0.5875 (pmm150)
REVERT: A  911 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6531 (ptt-90)
REVERT: A 1096 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7058 (mttp)
REVERT: C  531 MET cc_start: 0.7337 (mmt) cc_final: 0.6770 (mpt)
REVERT: D  531 MET cc_start: 0.6117 (mtt) cc_final: 0.5873 (OUTLIER)
REVERT: E  548 ASN cc_start: 0.6963 (m-40) cc_final: 0.6417 (t160)
REVERT: E  575 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8390 (mtt)
REVERT: E  694 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7148 (pt)
  outliers start: 17
  outliers final: 3
  residues processed: 227
  average time/residue: 0.6839
  time to fit residues: 168.3641
Evaluate side-chains
  211 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 205
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  911 ARG
Chi-restraints excluded: chain A residue 1096 LYS
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain E residue  575 MET
Chi-restraints excluded: chain E residue  694 ILE
Chi-restraints excluded: chain F residue  557 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 161 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 120 optimal weight:    0.8980
   chunk 134 optimal weight:    3.9990
   chunk 170 optimal weight:   10.0000
   chunk 122 optimal weight:    0.7980
   chunk 158 optimal weight:    2.9990
   chunk 176 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 904 GLN
A1394 GLN
E 632 GLN
F 499 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.194873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.144850 restraints weight = 13221.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 1.61
r_work: 0.3563 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14838  Z= 0.145
  Angle     :  0.570  12.408  20046  Z= 0.294
  Chirality :  0.041   0.162   2277
  Planarity :  0.004   0.056   2565
  Dihedral  :  4.573  24.016   1951
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.24 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.67 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.20), residues: 1792
  helix:  1.57 (0.16), residues: 1049
  sheet:  0.48 (0.50), residues: 91
  loop : -0.40 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1117 
 TYR   0.018   0.002   TYR A 529 
 PHE   0.024   0.001   PHE A 399 
 TRP   0.014   0.002   TRP A 754 
 HIS   0.004   0.001   HIS D 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (14830)
  covalent geometry    : angle       0.56988 (20043)
  SS BOND              : bond        0.00222 (    1)
  SS BOND              : angle       1.01317 (    2)
  hydrogen bonds       : bond        0.04933 (  823)
  hydrogen bonds       : angle       4.40627 ( 2355)
  metal coordination   : bond        0.00377 (    7)
  metal coordination   : angle       0.60980 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 212
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.7497 (tpt90)
REVERT: A  803 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7637 (tp40)
REVERT: A  911 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6536 (ptt-90)
REVERT: A 1082 ARG cc_start: 0.7193 (ttm110) cc_final: 0.6899 (ttp-110)
REVERT: A 1096 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7086 (mttp)
REVERT: A 1134 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7705 (mt)
REVERT: C  531 MET cc_start: 0.7267 (mmt) cc_final: 0.6694 (mpt)
REVERT: D  531 MET cc_start: 0.6183 (mtt) cc_final: 0.5942 (tpp)
REVERT: D  575 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8480 (mtm)
REVERT: D  581 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8074 (ttmm)
REVERT: E  641 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6531 (tm-30)
REVERT: E  694 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7151 (pt)
REVERT: F  518 MET cc_start: 0.6044 (ptm) cc_final: 0.5718 (ptm)
REVERT: F  535 HIS cc_start: 0.7125 (OUTLIER) cc_final: 0.6051 (m170)
  outliers start: 25
  outliers final: 4
  residues processed: 223
  average time/residue: 0.7363
  time to fit residues: 177.6829
Evaluate side-chains
  219 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 207
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  911 ARG
Chi-restraints excluded: chain A residue 1096 LYS
Chi-restraints excluded: chain A residue 1134 ILE
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain A residue 1331 ASP
Chi-restraints excluded: chain D residue  575 MET
Chi-restraints excluded: chain D residue  581 LYS
Chi-restraints excluded: chain E residue  577 MET
Chi-restraints excluded: chain E residue  641 GLU
Chi-restraints excluded: chain E residue  676 GLU
Chi-restraints excluded: chain E residue  694 ILE
Chi-restraints excluded: chain F residue  535 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 164 optimal weight:    7.9990
   chunk 8 optimal weight:    0.5980
   chunk 147 optimal weight:    2.9990
   chunk 173 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 130 optimal weight:   20.0000
   chunk 93 optimal weight:    2.9990
   chunk 126 optimal weight:    0.1980
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0870
   chunk 115 optimal weight:    6.9990
   overall best weight:    0.9760

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

Flipped N/Q/H residues before XYZ refinement:
A 139 GLN
A 858 GLN
A 876 ASN
A1394 GLN
E 632 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.194078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.141903 restraints weight = 21280.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 3.58
r_work: 0.3491 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3371
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14838  Z= 0.160
  Angle     :  0.580  12.868  20046  Z= 0.299
  Chirality :  0.042   0.169   2277
  Planarity :  0.004   0.053   2565
  Dihedral  :  4.586  23.575   1951
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.30 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.01 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.20), residues: 1792
  helix:  1.60 (0.16), residues: 1052
  sheet:  0.44 (0.50), residues: 91
  loop : -0.34 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1295 
 TYR   0.016   0.002   TYR A 529 
 PHE   0.025   0.002   PHE A 399 
 TRP   0.016   0.002   TRP A 754 
 HIS   0.004   0.001   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (14830)
  covalent geometry    : angle       0.57979 (20043)
  SS BOND              : bond        0.00156 (    1)
  SS BOND              : angle       0.91070 (    2)
  hydrogen bonds       : bond        0.04878 (  823)
  hydrogen bonds       : angle       4.34233 ( 2355)
  metal coordination   : bond        0.00445 (    7)
  metal coordination   : angle       0.74853 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 208
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7408 (tpt90)
REVERT: A  803 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7510 (tp40)
REVERT: A  911 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6580 (ptt-90)
REVERT: A 1082 ARG cc_start: 0.7116 (ttm110) cc_final: 0.6793 (ttp-110)
REVERT: A 1096 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6856 (mttp)
REVERT: A 1134 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7529 (mt)
REVERT: C  531 MET cc_start: 0.7219 (mmt) cc_final: 0.6642 (mpt)
REVERT: D  531 MET cc_start: 0.6051 (mtt) cc_final: 0.5831 (tpp)
REVERT: D  575 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8566 (mtm)
REVERT: D  581 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8058 (ttmm)
REVERT: F  518 MET cc_start: 0.5992 (ptm) cc_final: 0.5687 (ptm)
REVERT: F  535 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6004 (m170)
  outliers start: 30
  outliers final: 6
  residues processed: 222
  average time/residue: 0.7789
  time to fit residues: 187.0225
Evaluate side-chains
  211 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 199
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  722 ASP
Chi-restraints excluded: chain A residue  911 ARG
Chi-restraints excluded: chain A residue 1096 LYS
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain A residue 1134 ILE
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain A residue 1329 ASP
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain D residue  575 MET
Chi-restraints excluded: chain D residue  581 LYS
Chi-restraints excluded: chain E residue  676 GLU
Chi-restraints excluded: chain F residue  535 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 139 optimal weight:   30.0000
   chunk 130 optimal weight:   30.0000
   chunk 143 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 121 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 129 optimal weight:    7.9990
   chunk 174 optimal weight:    0.3980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 380 HIS
A 858 GLN
A 876 ASN
A1394 GLN
E 632 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.194863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.142884 restraints weight = 19952.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 3.22
r_work: 0.3512 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3393
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14838  Z= 0.140
  Angle     :  0.558  12.134  20046  Z= 0.287
  Chirality :  0.041   0.157   2277
  Planarity :  0.004   0.051   2565
  Dihedral  :  4.481  22.764   1951
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.24 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.29 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.20), residues: 1792
  helix:  1.78 (0.16), residues: 1046
  sheet:  0.44 (0.50), residues: 91
  loop : -0.33 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1295 
 TYR   0.020   0.002   TYR A 470 
 PHE   0.024   0.001   PHE A 399 
 TRP   0.014   0.002   TRP A 754 
 HIS   0.003   0.001   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (14830)
  covalent geometry    : angle       0.55781 (20043)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.84957 (    2)
  hydrogen bonds       : bond        0.04558 (  823)
  hydrogen bonds       : angle       4.23656 ( 2355)
  metal coordination   : bond        0.00366 (    7)
  metal coordination   : angle       0.50911 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 211
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.7850 (mtp-110) cc_final: 0.7408 (tpt90)
REVERT: A  376 LYS cc_start: 0.7478 (mptt) cc_final: 0.7273 (mptt)
REVERT: A  803 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7505 (tp40)
REVERT: A  911 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6540 (ptt-90)
REVERT: A 1082 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6727 (ttp-110)
REVERT: A 1096 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6859 (mttp)
REVERT: A 1134 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7542 (mt)
REVERT: A 1161 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7555 (ttt90)
REVERT: A 1442 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7224 (mm-30)
REVERT: C  531 MET cc_start: 0.7216 (mmt) cc_final: 0.6640 (mpt)
REVERT: D  531 MET cc_start: 0.6050 (mtt) cc_final: 0.5825 (tpp)
REVERT: D  575 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8556 (mtm)
REVERT: D  581 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8014 (ttmm)
REVERT: F  518 MET cc_start: 0.6027 (ptm) cc_final: 0.5764 (ptm)
REVERT: F  535 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6023 (m170)
  outliers start: 31
  outliers final: 9
  residues processed: 226
  average time/residue: 0.7601
  time to fit residues: 185.8853
Evaluate side-chains
  219 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 202
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  722 ASP
Chi-restraints excluded: chain A residue  822 ASN
Chi-restraints excluded: chain A residue  911 ARG
Chi-restraints excluded: chain A residue 1096 LYS
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain A residue 1134 ILE
Chi-restraints excluded: chain A residue 1161 ARG
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain A residue 1329 ASP
Chi-restraints excluded: chain A residue 1442 GLU
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain D residue  575 MET
Chi-restraints excluded: chain D residue  581 LYS
Chi-restraints excluded: chain E residue  632 GLN
Chi-restraints excluded: chain F residue  535 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0170
   chunk 77 optimal weight:    0.6980
   chunk 157 optimal weight:    4.9990
   chunk 126 optimal weight:    0.0040
   chunk 25 optimal weight:    0.8980
   chunk 112 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.4630

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

Flipped N/Q/H residues before XYZ refinement:
A 858 GLN
A 876 ASN
A 929 ASN
A1394 GLN
E 632 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.196236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.143709 restraints weight = 18758.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 2.99
r_work: 0.3527 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3412
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3412 r_free = 0.3412    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3412 r_free = 0.3412    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3412
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14838  Z= 0.117
  Angle     :  0.530  11.339  20046  Z= 0.273
  Chirality :  0.040   0.140   2277
  Planarity :  0.004   0.050   2565
  Dihedral  :  4.350  21.585   1951
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.07 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.08 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.20), residues: 1792
  helix:  1.94 (0.16), residues: 1054
  sheet:  0.53 (0.51), residues: 91
  loop : -0.29 (0.25), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1295 
 TYR   0.013   0.001   TYR A 732 
 PHE   0.022   0.001   PHE A 399 
 TRP   0.011   0.001   TRP A1248 
 HIS   0.002   0.001   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (14830)
  covalent geometry    : angle       0.53037 (20043)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       0.81604 (    2)
  hydrogen bonds       : bond        0.04176 (  823)
  hydrogen bonds       : angle       4.13373 ( 2355)
  metal coordination   : bond        0.00287 (    7)
  metal coordination   : angle       0.12902 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 218
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.6750 (p0) cc_final: 0.6502 (p0)
REVERT: A  141 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7456 (tpt90)
REVERT: A  204 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8136 (pptt)
REVERT: A  469 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6973 (pmt)
REVERT: A  587 ASP cc_start: 0.5805 (p0) cc_final: 0.5598 (p0)
REVERT: A  803 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7525 (tp40)
REVERT: A  911 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6533 (ptt-90)
REVERT: A 1096 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6965 (mttp)
REVERT: A 1134 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7651 (mt)
REVERT: A 1442 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7197 (mm-30)
REVERT: C  531 MET cc_start: 0.7254 (mmt) cc_final: 0.6669 (mpt)
REVERT: D  531 MET cc_start: 0.6086 (mtt) cc_final: 0.5872 (tpp)
REVERT: D  575 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8558 (mtm)
REVERT: E  641 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6118 (tm-30)
REVERT: F  479 MET cc_start: 0.5976 (tmm) cc_final: 0.5354 (tmm)
REVERT: F  518 MET cc_start: 0.6120 (ptm) cc_final: 0.5864 (ptm)
REVERT: F  535 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6047 (m170)
  outliers start: 29
  outliers final: 10
  residues processed: 234
  average time/residue: 0.7283
  time to fit residues: 184.3495
Evaluate side-chains
  228 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 209
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  911 ARG
Chi-restraints excluded: chain A residue 1096 LYS
Chi-restraints excluded: chain A residue 1134 ILE
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain A residue 1329 ASP
Chi-restraints excluded: chain A residue 1442 GLU
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain D residue  575 MET
Chi-restraints excluded: chain E residue  632 GLN
Chi-restraints excluded: chain E residue  641 GLU
Chi-restraints excluded: chain E residue  676 GLU
Chi-restraints excluded: chain F residue  535 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 78 optimal weight:    0.2980
   chunk 92 optimal weight:    0.7980
   chunk 105 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 157 optimal weight:    5.9990
   chunk 113 optimal weight:    0.3980
   chunk 131 optimal weight:    6.9990
   chunk 134 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 858 GLN
A 876 ASN
A 929 ASN
A1011 ASN
A1394 GLN
E 632 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.195564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.143673 restraints weight = 20734.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 3.31
r_work: 0.3522 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3408
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3408
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14838  Z= 0.133
  Angle     :  0.550  11.962  20046  Z= 0.282
  Chirality :  0.041   0.153   2277
  Planarity :  0.004   0.049   2565
  Dihedral  :  4.355  21.353   1951
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.13 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.81 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.20), residues: 1792
  helix:  1.95 (0.16), residues: 1052
  sheet:  0.51 (0.51), residues: 91
  loop : -0.29 (0.25), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1295 
 TYR   0.018   0.002   TYR A 470 
 PHE   0.024   0.001   PHE A 399 
 TRP   0.013   0.002   TRP A 754 
 HIS   0.003   0.001   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (14830)
  covalent geometry    : angle       0.55017 (20043)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       0.79893 (    2)
  hydrogen bonds       : bond        0.04316 (  823)
  hydrogen bonds       : angle       4.14833 ( 2355)
  metal coordination   : bond        0.00351 (    7)
  metal coordination   : angle       0.13435 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 212
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7401 (tpt90)
REVERT: A  204 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8147 (pptt)
REVERT: A  469 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6978 (pmt)
REVERT: A  803 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7499 (tp40)
REVERT: A  911 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6504 (ptt-90)
REVERT: A 1096 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6913 (mttp)
REVERT: A 1134 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7622 (mt)
REVERT: A 1161 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7516 (ttt90)
REVERT: A 1442 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7186 (mm-30)
REVERT: C  531 MET cc_start: 0.7218 (mmt) cc_final: 0.6639 (mpt)
REVERT: D  531 MET cc_start: 0.6039 (mtt) cc_final: 0.5837 (tpp)
REVERT: D  575 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8558 (mtm)
REVERT: E  531 MET cc_start: 0.7860 (ttp) cc_final: 0.7335 (tpt)
REVERT: F  479 MET cc_start: 0.5959 (tmm) cc_final: 0.5651 (tmm)
REVERT: F  518 MET cc_start: 0.6069 (ptm) cc_final: 0.5819 (ptm)
REVERT: F  535 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6019 (m170)
  outliers start: 33
  outliers final: 10
  residues processed: 229
  average time/residue: 0.7310
  time to fit residues: 181.2681
Evaluate side-chains
  231 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 212
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  503 ARG
Chi-restraints excluded: chain A residue  722 ASP
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  911 ARG
Chi-restraints excluded: chain A residue 1096 LYS
Chi-restraints excluded: chain A residue 1134 ILE
Chi-restraints excluded: chain A residue 1161 ARG
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain A residue 1329 ASP
Chi-restraints excluded: chain A residue 1442 GLU
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain D residue  575 MET
Chi-restraints excluded: chain F residue  535 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 150 optimal weight:   10.0000
   chunk 102 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 155 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 858 GLN
A 876 ASN
A1394 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.192977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.140744 restraints weight = 14875.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.18
r_work: 0.3544 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3417 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14838  Z= 0.190
  Angle     :  0.618  13.499  20046  Z= 0.316
  Chirality :  0.044   0.196   2277
  Planarity :  0.004   0.048   2565
  Dihedral  :  4.598  22.889   1951
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.41 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.29 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.20), residues: 1792
  helix:  1.73 (0.16), residues: 1052
  sheet:  0.41 (0.50), residues: 91
  loop : -0.34 (0.25), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1295 
 TYR   0.019   0.002   TYR A 407 
 PHE   0.026   0.002   PHE A 399 
 TRP   0.019   0.002   TRP A 754 
 HIS   0.004   0.001   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (14830)
  covalent geometry    : angle       0.61804 (20043)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.77653 (    2)
  hydrogen bonds       : bond        0.05007 (  823)
  hydrogen bonds       : angle       4.30349 ( 2355)
  metal coordination   : bond        0.00594 (    7)
  metal coordination   : angle       1.09270 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 212
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7454 (tpt90)
REVERT: A  204 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8130 (pptt)
REVERT: A  460 GLU cc_start: 0.6266 (mp0) cc_final: 0.6046 (mp0)
REVERT: A  469 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6887 (pmt)
REVERT: A  803 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7698 (tp40)
REVERT: A  911 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6595 (ptt-90)
REVERT: A  969 GLU cc_start: 0.7685 (tp30) cc_final: 0.7112 (pm20)
REVERT: A 1096 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7022 (mttp)
REVERT: A 1132 GLU cc_start: 0.7306 (tm-30) cc_final: 0.7106 (mt-10)
REVERT: A 1134 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7681 (mt)
REVERT: A 1161 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7610 (ttt90)
REVERT: A 1442 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7104 (mm-30)
REVERT: C  531 MET cc_start: 0.7297 (mmt) cc_final: 0.6721 (mpt)
REVERT: D  531 MET cc_start: 0.6176 (mtt) cc_final: 0.5968 (tpp)
REVERT: D  575 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8571 (mtm)
REVERT: E  531 MET cc_start: 0.7834 (ttp) cc_final: 0.7339 (tpt)
REVERT: F  479 MET cc_start: 0.5975 (tmm) cc_final: 0.5231 (mmm)
REVERT: F  518 MET cc_start: 0.6063 (ptm) cc_final: 0.5782 (ptm)
  outliers start: 30
  outliers final: 12
  residues processed: 225
  average time/residue: 0.7078
  time to fit residues: 172.6817
Evaluate side-chains
  226 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  503 ARG
Chi-restraints excluded: chain A residue  713 ASP
Chi-restraints excluded: chain A residue  722 ASP
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  911 ARG
Chi-restraints excluded: chain A residue 1096 LYS
Chi-restraints excluded: chain A residue 1134 ILE
Chi-restraints excluded: chain A residue 1161 ARG
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain A residue 1329 ASP
Chi-restraints excluded: chain A residue 1372 ILE
Chi-restraints excluded: chain A residue 1442 GLU
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain D residue  575 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 147 optimal weight:    2.9990
   chunk 108 optimal weight:    0.1980
   chunk 55 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 170 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 139 optimal weight:   30.0000
   chunk 56 optimal weight:    0.9990
   chunk 175 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 858 GLN
A 876 ASN
A1394 GLN
E 632 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.194932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.142509 restraints weight = 18362.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 2.84
r_work: 0.3521 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3408
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3408
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14838  Z= 0.135
  Angle     :  0.571  12.291  20046  Z= 0.291
  Chirality :  0.041   0.193   2277
  Planarity :  0.004   0.045   2565
  Dihedral  :  4.446  21.668   1951
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.19 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.84 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.20), residues: 1792
  helix:  1.92 (0.16), residues: 1045
  sheet:  0.51 (0.50), residues: 91
  loop : -0.27 (0.25), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1295 
 TYR   0.016   0.001   TYR A1448 
 PHE   0.024   0.001   PHE A 399 
 TRP   0.013   0.002   TRP A 754 
 HIS   0.004   0.001   HIS A  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (14830)
  covalent geometry    : angle       0.57066 (20043)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.81413 (    2)
  hydrogen bonds       : bond        0.04388 (  823)
  hydrogen bonds       : angle       4.18841 ( 2355)
  metal coordination   : bond        0.00339 (    7)
  metal coordination   : angle       0.29177 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 211
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.7434 (tpt90)
REVERT: A  204 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8091 (pptt)
REVERT: A  460 GLU cc_start: 0.6350 (mp0) cc_final: 0.6133 (mp0)
REVERT: A  469 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7005 (pmt)
REVERT: A  803 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7563 (tp40)
REVERT: A  911 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6515 (ptt-90)
REVERT: A  969 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7118 (pm20)
REVERT: A 1096 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6974 (mttp)
REVERT: A 1132 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7108 (mt-10)
REVERT: A 1134 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7673 (mt)
REVERT: A 1161 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7570 (ttt90)
REVERT: A 1442 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7130 (mm-30)
REVERT: C  531 MET cc_start: 0.7282 (mmt) cc_final: 0.6701 (mpt)
REVERT: D  531 MET cc_start: 0.6162 (mtt) cc_final: 0.5934 (tpp)
REVERT: D  575 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8555 (mtm)
REVERT: E  689 GLU cc_start: 0.6567 (mp0) cc_final: 0.6309 (tp30)
REVERT: F  479 MET cc_start: 0.5999 (tmm) cc_final: 0.5243 (mmm)
REVERT: F  518 MET cc_start: 0.6173 (ptm) cc_final: 0.5899 (ptm)
  outliers start: 24
  outliers final: 11
  residues processed: 221
  average time/residue: 0.7415
  time to fit residues: 177.3936
Evaluate side-chains
  225 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 205
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  503 ARG
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  888 LEU
Chi-restraints excluded: chain A residue  911 ARG
Chi-restraints excluded: chain A residue  969 GLU
Chi-restraints excluded: chain A residue 1096 LYS
Chi-restraints excluded: chain A residue 1134 ILE
Chi-restraints excluded: chain A residue 1161 ARG
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain A residue 1329 ASP
Chi-restraints excluded: chain A residue 1372 ILE
Chi-restraints excluded: chain A residue 1442 GLU
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain D residue  575 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 145 optimal weight:    8.9990
   chunk 76 optimal weight:    0.1980
   chunk 159 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 172 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0270
   chunk 161 optimal weight:    0.7980
   chunk 92 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A 876 ASN
A1394 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.196554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.144780 restraints weight = 22529.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 3.54
r_work: 0.3518 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3397
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14838  Z= 0.119
  Angle     :  0.555  11.117  20046  Z= 0.282
  Chirality :  0.040   0.168   2277
  Planarity :  0.004   0.045   2565
  Dihedral  :  4.301  22.393   1951
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.35 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 15.27 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.20), residues: 1792
  helix:  2.01 (0.16), residues: 1055
  sheet:  0.59 (0.51), residues: 91
  loop : -0.25 (0.25), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1295 
 TYR   0.020   0.001   TYR A 470 
 PHE   0.022   0.001   PHE A 399 
 TRP   0.011   0.001   TRP A1248 
 HIS   0.005   0.001   HIS A  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (14830)
  covalent geometry    : angle       0.55521 (20043)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       0.79414 (    2)
  hydrogen bonds       : bond        0.04028 (  823)
  hydrogen bonds       : angle       4.08419 ( 2355)
  metal coordination   : bond        0.00369 (    7)
  metal coordination   : angle       0.26354 (    1)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 207
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.7834 (mtp-110) cc_final: 0.7397 (tpt90)
REVERT: A  204 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8064 (pptt)
REVERT: A  469 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7028 (pmt)
REVERT: A  803 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7475 (tp40)
REVERT: A  911 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6490 (ptt-90)
REVERT: A  969 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7289 (tp30)
REVERT: A 1096 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6870 (mttp)
REVERT: A 1103 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7394 (mp0)
REVERT: A 1161 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7471 (ttt90)
REVERT: C  531 MET cc_start: 0.7221 (mmt) cc_final: 0.6636 (mpt)
REVERT: D  575 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8563 (mtm)
REVERT: E  531 MET cc_start: 0.7882 (ttp) cc_final: 0.7333 (tpt)
REVERT: E  689 GLU cc_start: 0.6529 (mp0) cc_final: 0.6284 (tp30)
REVERT: F  479 MET cc_start: 0.5929 (tmm) cc_final: 0.5345 (mmm)
REVERT: F  518 MET cc_start: 0.6127 (ptm) cc_final: 0.5858 (ptm)
REVERT: F  535 HIS cc_start: 0.7045 (OUTLIER) cc_final: 0.6010 (m170)
  outliers start: 20
  outliers final: 9
  residues processed: 217
  average time/residue: 0.6965
  time to fit residues: 163.9086
Evaluate side-chains
  222 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  888 LEU
Chi-restraints excluded: chain A residue  911 ARG
Chi-restraints excluded: chain A residue  969 GLU
Chi-restraints excluded: chain A residue 1096 LYS
Chi-restraints excluded: chain A residue 1161 ARG
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain A residue 1329 ASP
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain D residue  575 MET
Chi-restraints excluded: chain F residue  535 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 147 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 121 optimal weight:    0.0470
   chunk 124 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 132 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0980
   chunk 133 optimal weight:    4.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A 876 ASN
A1011 ASN
A1394 GLN
** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 535 HIS
E 632 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.196560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.144944 restraints weight = 16456.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 2.38
r_work: 0.3579 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14838  Z= 0.121
  Angle     :  0.566  11.271  20046  Z= 0.287
  Chirality :  0.040   0.193   2277
  Planarity :  0.004   0.047   2565
  Dihedral  :  4.274  22.474   1951
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.13 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.33 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.20), residues: 1792
  helix:  2.06 (0.16), residues: 1055
  sheet:  0.55 (0.50), residues: 91
  loop : -0.24 (0.25), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1295 
 TYR   0.014   0.001   TYR A1448 
 PHE   0.023   0.001   PHE A 399 
 TRP   0.010   0.001   TRP A 754 
 HIS   0.006   0.001   HIS D 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (14830)
  covalent geometry    : angle       0.56582 (20043)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       0.79082 (    2)
  hydrogen bonds       : bond        0.04024 (  823)
  hydrogen bonds       : angle       4.08347 ( 2355)
  metal coordination   : bond        0.00351 (    7)
  metal coordination   : angle       0.32879 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7832.89 seconds
wall clock time: 133 minutes 46.35 seconds (8026.35 seconds total)