Starting phenix.real_space_refine
on Wed Mar 12 21:51:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ket_37167/03_2025/8ket_37167.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ket_37167/03_2025/8ket_37167.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ket_37167/03_2025/8ket_37167.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ket_37167/03_2025/8ket_37167.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ket_37167/03_2025/8ket_37167.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ket_37167/03_2025/8ket_37167.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    5200      2.51       5
     N    1531      2.21       5
     O    1643      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8399
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 1323
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 233}
          Link IDs: {'PTRANS': 7, 'TRANS': 258}
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 918
          Unresolved non-hydrogen angles: 1184
          Unresolved non-hydrogen dihedrals: 798
          Unresolved non-hydrogen chiralities: 90
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 8, 'TYR:plan': 13, 'ASN:plan1': 3, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 27, 'GLU:plan': 9, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 487
    Chain: "B"
      Number of atoms: 1436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1436
          Classifications: {'peptide': 267}
          Incomplete info: {'truncation_to_alanine': 205}
          Link IDs: {'PTRANS': 7, 'TRANS': 259}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 805
          Unresolved non-hydrogen angles: 1034
          Unresolved non-hydrogen dihedrals: 697
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 25, 'GLU:plan': 9, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 427
    Chain: "F"
      Number of atoms: 1801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 1801
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 21, 'TRANS': 234}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 299
          Unresolved non-hydrogen angles: 372
          Unresolved non-hydrogen dihedrals: 248
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 175
    Chain: "H"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 18
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
    Chain: "C"
      Number of atoms: 3682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 3682
          Classifications: {'peptide': 537}
          Incomplete info: {'truncation_to_alanine': 142}
          Link IDs: {'PTRANS': 9, 'TRANS': 527}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 578
          Unresolved non-hydrogen angles: 734
          Unresolved non-hydrogen dihedrals: 498
          Unresolved non-hydrogen chiralities: 31
          Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 5, 'TYR:plan': 14, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 366
    Chain: "D"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 2, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 6.22, per 1000 atoms: 0.74
  Number of scatterers: 8399
  At special positions: 0
  Unit cell: (98.44, 105.93, 148.73, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1643      8.00
     N    1531      7.00
     C    5200      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  79 " - pdb=" SG  CYS F 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 113 " - pdb=" SG  CYS F 126 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 199 " - pdb=" SG  CYS F 232 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 311 " - pdb=" SG  CYS C 539 " distance=2.02

  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
  Links applied
    ALPHA1-4
      " NAG D   2 " - " MAN D   3 "
    ALPHA1-6
      " MAN D   3 " - " MAN D   4 "
      " MAN D   4 " - " MAN D   6 "
    BETA1-3
      " NAG D   1 " - " NAG D   2 "
      " MAN D   4 " - " BMA D   5 "
    BETA1-4
      " MAN D   3 " - " BMA D   7 "
    NAG-ASN
      " NAG C 801 " - " ASN C 217 "
      " NAG C 802 " - " ASN C 272 "
      " NAG C 803 " - " ASN C 431 "
      " NAG C 804 " - " ASN C 608 "
      " NAG D   1 " - " ASN H 350 "
  Time building additional restraints: 2.77
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2496

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 5 sheets defined
      72.7% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 26
      removed outlier: 4.209A  pdb=" N   LEU A  25 " --> pdb=" O   HIS A  21 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS A  26 " --> pdb=" O   ALA A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 39
    Processing helix  chain 'A' and resid 39 through 66
    Processing helix  chain 'A' and resid 72 through 96
      removed outlier: 3.672A  pdb=" N   THR A  86 " --> pdb=" O   TRP A  82 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ARG A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 130
      removed outlier: 4.007A  pdb=" N   VAL A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ALA A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   LEU A 106 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 166
    Processing helix  chain 'A' and resid 169 through 200
      removed outlier: 4.230A  pdb=" N   VAL A 173 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 237
      removed outlier: 4.403A  pdb=" N   ALA A 209 " --> pdb=" O   TRP A 205 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   VAL A 210 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 266
      removed outlier: 3.564A  pdb=" N   TYR A 249 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 26
      removed outlier: 3.512A  pdb=" N   MET B   7 " --> pdb=" O   ARG B   3 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU B  14 " --> pdb=" O   ALA B  10 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA B  20 " --> pdb=" O   GLY B  16 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   HIS B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   TYR B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU B  25 " --> pdb=" O   HIS B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 37
    Processing helix  chain 'B' and resid 39 through 66
      removed outlier: 3.712A  pdb=" N   VAL B  45 " --> pdb=" O   PRO B  41 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU B  46 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU B  56 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LYS B  63 " --> pdb=" O   LYS B  59 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE B  65 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   PHE B  66 " --> pdb=" O   GLY B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 95
      removed outlier: 3.671A  pdb=" N   TYR B  83 " --> pdb=" O   GLU B  79 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR B  93 " --> pdb=" O   CYS B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 130
      removed outlier: 3.550A  pdb=" N   ALA B 105 " --> pdb=" O   PRO B 101 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU B 106 " --> pdb=" O   ARG B 102 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU B 111 " --> pdb=" O   PHE B 107 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLU B 128 " --> pdb=" O   VAL B 124 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG B 129 " --> pdb=" O   ASP B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 166
    Processing helix  chain 'B' and resid 169 through 201
      removed outlier: 4.294A  pdb=" N   VAL B 173 " --> pdb=" O   SER B 169 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER B 201 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 236
      removed outlier: 4.444A  pdb=" N   VAL B 210 " --> pdb=" O   ASP B 206 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE B 230 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 267
    Processing helix  chain 'F' and resid 99 through 111
      removed outlier: 3.913A  pdb=" N   LEU F 103 " --> pdb=" O   ASN F  99 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU F 104 " --> pdb=" O   PRO F 100 " (cutoff:3.500A)
      Proline residue:  F 106  - end of helix
      removed outlier: 3.799A  pdb=" N   SER F 111 " --> pdb=" O   LEU F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 169
      removed outlier: 3.604A  pdb=" N   LEU F 160 " --> pdb=" O   ALA F 156 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 241 through 246
      removed outlier: 4.401A  pdb=" N   SER F 245 " --> pdb=" O   LEU F 242 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 271 through 286
      removed outlier: 3.636A  pdb=" N   VAL F 286 " --> pdb=" O   GLU F 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 197
      removed outlier: 3.620A  pdb=" N   ILE C 193 " --> pdb=" O   THR C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 216
      removed outlier: 3.701A  pdb=" N   TYR C 209 " --> pdb=" O   GLU C 205 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LYS C 212 " --> pdb=" O   ARG C 208 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   MET C 216 " --> pdb=" O   LYS C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 218 through 232
      removed outlier: 3.810A  pdb=" N   ARG C 224 " --> pdb=" O   LYS C 220 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   TYR C 227 " --> pdb=" O   GLU C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 253
      removed outlier: 3.587A  pdb=" N   GLU C 251 " --> pdb=" O   GLU C 247 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLU C 252 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 268
      removed outlier: 3.810A  pdb=" N   ALA C 260 " --> pdb=" O   LYS C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 274 through 288
      removed outlier: 3.638A  pdb=" N   VAL C 280 " --> pdb=" O   ALA C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 304
      removed outlier: 3.582A  pdb=" N   TRP C 302 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 310 through 329
      removed outlier: 3.653A  pdb=" N   HIS C 317 " --> pdb=" O   SER C 313 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU C 320 " --> pdb=" O   THR C 316 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   VAL C 321 " --> pdb=" O   HIS C 317 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 348
    Processing helix  chain 'C' and resid 362 through 370
    Processing helix  chain 'C' and resid 372 through 385
    Processing helix  chain 'C' and resid 393 through 408
      removed outlier: 3.656A  pdb=" N   ALA C 407 " --> pdb=" O   LEU C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 409 through 423
    Processing helix  chain 'C' and resid 430 through 445
      removed outlier: 3.828A  pdb=" N   ALA C 434 " --> pdb=" O   SER C 430 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   MET C 444 " --> pdb=" O   LYS C 440 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLY C 445 " --> pdb=" O   ALA C 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 446 through 460
    Processing helix  chain 'C' and resid 466 through 481
      removed outlier: 3.740A  pdb=" N   LYS C 476 " --> pdb=" O   LYS C 472 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 482 through 495
      removed outlier: 3.516A  pdb=" N   LEU C 487 " --> pdb=" O   VAL C 483 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN C 488 " --> pdb=" O   ASP C 484 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   MET C 492 " --> pdb=" O   GLN C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 502 through 516
      removed outlier: 3.768A  pdb=" N   GLN C 515 " --> pdb=" O   ASN C 511 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY C 516 " --> pdb=" O   LEU C 512 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 518 through 532
      removed outlier: 3.524A  pdb=" N   SER C 531 " --> pdb=" O   GLN C 527 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 538 through 551
      removed outlier: 3.796A  pdb=" N   ALA C 542 " --> pdb=" O   SER C 538 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASN C 548 " --> pdb=" O   GLU C 544 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL C 549 " --> pdb=" O   LEU C 545 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 557 through 568
    Processing helix  chain 'C' and resid 571 through 585
      removed outlier: 3.536A  pdb=" N   VAL C 575 " --> pdb=" O   TYR C 571 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ILE C 576 " --> pdb=" O   ASN C 572 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLN C 577 " --> pdb=" O   ALA C 573 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TYR C 578 " --> pdb=" O   ALA C 574 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU C 581 " --> pdb=" O   GLN C 577 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 587 through 599
      removed outlier: 3.912A  pdb=" N   ALA C 594 " --> pdb=" O   GLN C 590 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 609 through 623
      removed outlier: 3.813A  pdb=" N   HIS C 617 " --> pdb=" O   ARG C 613 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 627 through 640
      removed outlier: 3.549A  pdb=" N   HIS C 637 " --> pdb=" O   LEU C 633 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 646 through 660
      removed outlier: 3.538A  pdb=" N   SER C 658 " --> pdb=" O   TYR C 654 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLN C 660 " --> pdb=" O   LEU C 656 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 663 through 677
      removed outlier: 3.582A  pdb=" N   MET C 667 " --> pdb=" O   SER C 663 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 683 through 698
      removed outlier: 3.863A  pdb=" N   ALA C 694 " --> pdb=" O   PHE C 690 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA C 695 " --> pdb=" O   TYR C 691 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 701 through 723
      removed outlier: 3.594A  pdb=" N   ALA C 708 " --> pdb=" O   PRO C 704 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 43 through 46
      removed outlier: 6.149A  pdb=" N   ARG F  44 " --> pdb=" O   ILE F 259 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   CYS F 261 " --> pdb=" O   ARG F  44 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ASN F  46 " --> pdb=" O   CYS F 261 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   SER F 263 " --> pdb=" O   ASN F  46 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   ASP F 258 " --> pdb=" O   PRO F  82 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE F 260 " --> pdb=" O   ILE F  80 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   ASN F  65 " --> pdb=" O   LEU F  81 " (cutoff:3.500A)
      removed outlier: 10.543A  pdb=" N   LEU F  83 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 10.941A  pdb=" N   GLU F  63 " --> pdb=" O   LEU F  83 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 122 through 125
      removed outlier: 6.057A  pdb=" N   ILE F 131 " --> pdb=" O   LEU F 151 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   TYR F 149 " --> pdb=" O   GLN F 133 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 178 through 181
    Processing sheet with id=AA4, first strand: chain 'F' and resid 189 through 193
      removed outlier: 7.310A  pdb=" N   SER F 208 " --> pdb=" O   TYR F 234 " (cutoff:3.500A)
      removed outlier: 8.732A  pdb=" N   VAL F 236 " --> pdb=" O   SER F 208 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   THR F 210 " --> pdb=" O   VAL F 236 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   ILE F 238 " --> pdb=" O   THR F 210 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   MET F 212 " --> pdb=" O   ILE F 238 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   THR F 240 " --> pdb=" O   MET F 212 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   ILE F 214 " --> pdb=" O   THR F 240 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   GLU F 233 " --> pdb=" O   GLU F 228 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   GLU F 228 " --> pdb=" O   GLU F 233 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   GLU F 235 " --> pdb=" O   VAL F 226 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   VAL F 226 " --> pdb=" O   GLU F 235 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   VAL F 237 " --> pdb=" O   LEU F 224 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 198 through 199
      removed outlier: 3.732A  pdb=" N   ARG F 205 " --> pdb=" O   CYS F 199 " (cutoff:3.500A)

    703 hydrogen bonds defined for protein.
    2091 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: 2.75

  Time building geometry restraints manager: 3.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2333
        1.34 -     1.46: 1558
        1.46 -     1.58: 4583
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 8512
  Sorted by residual:
  bond pdb=" CA  ARG C 689 "
       pdb=" C   ARG C 689 "
    ideal  model  delta    sigma   weight residual
    1.524  1.481  0.043 1.27e-02 6.20e+03 1.13e+01
  bond pdb=" C6  MAN D   4 "
       pdb=" O6  MAN D   4 "
    ideal  model  delta    sigma   weight residual
    1.407  1.466 -0.059 2.00e-02 2.50e+03 8.58e+00
  bond pdb=" CB  CYS C 539 "
       pdb=" SG  CYS C 539 "
    ideal  model  delta    sigma   weight residual
    1.808  1.723  0.085 3.30e-02 9.18e+02 6.68e+00
  bond pdb=" CA  LYS C 688 "
       pdb=" C   LYS C 688 "
    ideal  model  delta    sigma   weight residual
    1.524  1.494  0.030 1.29e-02 6.01e+03 5.31e+00
  bond pdb=" C1  NAG C 803 "
       pdb=" O5  NAG C 803 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.69e+00
  ... (remaining 8507 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 11280
        1.85 -     3.69: 339
        3.69 -     5.54: 50
        5.54 -     7.39: 11
        7.39 -     9.24: 5
  Bond angle restraints: 11685
  Sorted by residual:
  angle pdb=" CA  TYR B  23 "
        pdb=" CB  TYR B  23 "
        pdb=" CG  TYR B  23 "
      ideal   model   delta    sigma   weight residual
     113.90  120.42   -6.52 1.80e+00 3.09e-01 1.31e+01
  angle pdb=" CB  LYS F  74 "
        pdb=" CG  LYS F  74 "
        pdb=" CD  LYS F  74 "
      ideal   model   delta    sigma   weight residual
     111.30  119.37   -8.07 2.30e+00 1.89e-01 1.23e+01
  angle pdb=" C   GLN F 203 "
        pdb=" N   ASN F 204 "
        pdb=" CA  ASN F 204 "
      ideal   model   delta    sigma   weight residual
     122.46  127.17   -4.71 1.41e+00 5.03e-01 1.12e+01
  angle pdb=" CB  GLN C 240 "
        pdb=" CG  GLN C 240 "
        pdb=" CD  GLN C 240 "
      ideal   model   delta    sigma   weight residual
     112.60  117.87   -5.27 1.70e+00 3.46e-01 9.61e+00
  angle pdb=" N   GLU C 432 "
        pdb=" CA  GLU C 432 "
        pdb=" C   GLU C 432 "
      ideal   model   delta    sigma   weight residual
     111.07  114.18   -3.11 1.07e+00 8.73e-01 8.43e+00
  ... (remaining 11680 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.69: 4783
       25.69 -    51.38: 274
       51.38 -    77.07: 39
       77.07 -   102.76: 31
      102.76 -   128.45: 21
  Dihedral angle restraints: 5148
    sinusoidal: 1284
      harmonic: 3864
  Sorted by residual:
  dihedral pdb=" CA  CYS C 539 "
           pdb=" C   CYS C 539 "
           pdb=" N   HIS C 540 "
           pdb=" CA  HIS C 540 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.89  -26.11     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  CYS C 311 "
           pdb=" C   CYS C 311 "
           pdb=" N   GLU C 312 "
           pdb=" CA  GLU C 312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.13  -25.87     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  SER F  38 "
           pdb=" C   SER F  38 "
           pdb=" N   ASP F  39 "
           pdb=" CA  ASP F  39 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.04   23.96     0      5.00e+00 4.00e-02 2.30e+01
  ... (remaining 5145 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.257: 1446
       0.257 -    0.515: 0
       0.515 -    0.772: 1
       0.772 -    1.029: 0
       1.029 -    1.286: 1
  Chirality restraints: 1448
  Sorted by residual:
  chirality pdb=" C1  MAN D   3 "
            pdb=" O4  NAG D   2 "
            pdb=" C2  MAN D   3 "
            pdb=" O5  MAN D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    1.87    0.53 2.00e-02 2.50e+03 7.01e+02
  chirality pdb=" C1  MAN D   6 "
            pdb=" O6  MAN D   4 "
            pdb=" C2  MAN D   6 "
            pdb=" O5  MAN D   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.65   -0.25 2.00e-02 2.50e+03 1.53e+02
  chirality pdb=" C1  BMA D   7 "
            pdb=" O4  MAN D   3 "
            pdb=" C2  BMA D   7 "
            pdb=" O5  BMA D   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-02 2.50e+03 9.23e+01
  ... (remaining 1445 not shown)

  Planarity restraints: 1573
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.342 2.00e-02 2.50e+03   2.97e-01 1.10e+03
        pdb=" C7  NAG D   2 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.103 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.529 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.163 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.297 2.00e-02 2.50e+03   2.50e-01 7.80e+02
        pdb=" C7  NAG D   1 "    0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.187 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.427 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 608 "    0.032 2.00e-02 2.50e+03   3.07e-02 1.18e+01
        pdb=" CG  ASN C 608 "   -0.034 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 608 "    0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 608 "   -0.037 2.00e-02 2.50e+03
        pdb=" C1  NAG C 804 "    0.034 2.00e-02 2.50e+03
  ... (remaining 1570 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1822
        2.77 -     3.30: 7904
        3.30 -     3.84: 13859
        3.84 -     4.37: 14220
        4.37 -     4.90: 25501
  Nonbonded interactions: 63306
  Sorted by model distance:
  nonbonded pdb=" O   SER C 273 "
            pdb=" OG  SER C 273 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OD1 ASP C 635 "
            pdb=" OH  TYR C 654 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OD1 ASP C 598 "
            pdb=" OH  TYR C 636 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG1 THR F 122 "
            pdb=" O   TYR F 134 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OH  TYR F  61 "
            pdb=" O   ASP F 258 "
     model   vdw
     2.300 3.040
  ... (remaining 63301 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 'A' and (name N or name CA or name C or name O or name CB ))
  selection = (chain 'B' and ((resid 1 through 57 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 58 through 266))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.880
  Find NCS groups from input model:        0.210
  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:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6403
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   8512  Z= 0.275
  Angle     :  0.739   9.237  11685  Z= 0.401
  Chirality :  0.057   1.286   1448
  Planarity :  0.011   0.297   1568
  Dihedral  : 21.356 128.454   2640
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.80 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 26.75 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.20), residues: 1317
  helix: -0.99 (0.14), residues: 923
  sheet: -0.61 (0.60), residues: 81
  loop : -1.69 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 555 
 HIS   0.007   0.001   HIS C 540 
 PHE   0.009   0.001   PHE F 260 
 TYR   0.035   0.002   TYR F 123 
 ARG   0.014   0.001   ARG F 285 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  285 ARG cc_start: 0.6799 (ttp-110) cc_final: 0.6574 (ttm-80)
  outliers start: 8
  outliers final: 6
  residues processed: 138
  average time/residue: 0.1922
  time to fit residues: 37.2725
Evaluate side-chains
  137 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 131
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   84 VAL
Chi-restraints excluded: chain F residue  191 VAL
Chi-restraints excluded: chain F residue  269 PHE
Chi-restraints excluded: chain C residue  217 ASN
Chi-restraints excluded: chain C residue  340 ILE
Chi-restraints excluded: chain C residue  541 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:   30.0000
   chunk 66 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 101 optimal weight:    8.9990
   chunk 39 optimal weight:   40.0000
   chunk 61 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 118 optimal weight:    0.8980
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
F 130 HIS
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 624 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.268777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.241190 restraints weight = 9466.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.4656 rms_B_bonded: 1.14
r_work: 0.4280 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.087   8512  Z= 0.509
  Angle     :  0.731  10.395  11685  Z= 0.370
  Chirality :  0.048   0.376   1448
  Planarity :  0.006   0.069   1568
  Dihedral  : 15.795 115.532   1624
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.56 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 24.20 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.22), residues: 1317
  helix:  0.70 (0.16), residues: 933
  sheet: -0.92 (0.56), residues: 79
  loop : -1.79 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 302 
 HIS   0.011   0.002   HIS C 518 
 PHE   0.019   0.002   PHE C 668 
 TYR   0.020   0.002   TYR B  30 
 ARG   0.005   0.001   ARG F 132 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: F  258 ASP cc_start: 0.8014 (p0) cc_final: 0.7734 (p0)
REVERT: C  223 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.6447 (mp0)
REVERT: C  578 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8463 (m-10)
REVERT: C  587 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8104 (tm-30)
  outliers start: 27
  outliers final: 20
  residues processed: 151
  average time/residue: 0.1994
  time to fit residues: 41.4964
Evaluate side-chains
  146 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain F residue   84 VAL
Chi-restraints excluded: chain F residue  150 TYR
Chi-restraints excluded: chain F residue  191 VAL
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  208 SER
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  270 LYS
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain C residue  217 ASN
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  327 SER
Chi-restraints excluded: chain C residue  340 ILE
Chi-restraints excluded: chain C residue  528 MET
Chi-restraints excluded: chain C residue  541 THR
Chi-restraints excluded: chain C residue  549 VAL
Chi-restraints excluded: chain C residue  578 TYR
Chi-restraints excluded: chain C residue  587 GLU
Chi-restraints excluded: chain C residue  588 VAL
Chi-restraints excluded: chain C residue  607 GLU
Chi-restraints excluded: chain C residue  674 HIS
Chi-restraints excluded: chain C residue  683 ASP
Chi-restraints excluded: chain C residue  705 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 105 optimal weight:    8.9990
   chunk 110 optimal weight:    0.5980
   chunk 84 optimal weight:    0.4980
   chunk 125 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 121 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   chunk 48 optimal weight:   50.0000
   chunk 12 optimal weight:   40.0000
   chunk 18 optimal weight:   40.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.273912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4754 r_free = 0.4754 target = 0.252307 restraints weight = 9570.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.4749 rms_B_bonded: 1.16
r_work: 0.4358 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3981 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8512  Z= 0.183
  Angle     :  0.579   9.292  11685  Z= 0.282
  Chirality :  0.042   0.336   1448
  Planarity :  0.004   0.053   1568
  Dihedral  : 13.276 117.830   1622
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.49 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 25.90 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.23), residues: 1317
  helix:  1.64 (0.17), residues: 938
  sheet: -1.20 (0.56), residues: 79
  loop : -1.63 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP F 121 
 HIS   0.003   0.001   HIS C 518 
 PHE   0.009   0.001   PHE C 668 
 TYR   0.013   0.001   TYR F 120 
 ARG   0.003   0.000   ARG F 116 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   62 LYS cc_start: 0.7038 (tttm) cc_final: 0.6812 (tttt)
REVERT: F  258 ASP cc_start: 0.8352 (p0) cc_final: 0.7895 (p0)
REVERT: C  209 TYR cc_start: 0.6279 (m-80) cc_final: 0.6000 (m-80)
REVERT: C  235 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8486 (mp)
REVERT: C  598 ASP cc_start: 0.7907 (t70) cc_final: 0.7631 (t0)
  outliers start: 22
  outliers final: 13
  residues processed: 156
  average time/residue: 0.2224
  time to fit residues: 49.0677
Evaluate side-chains
  144 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain F residue  126 CYS
Chi-restraints excluded: chain F residue  150 TYR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  270 LYS
Chi-restraints excluded: chain C residue  217 ASN
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  607 GLU
Chi-restraints excluded: chain C residue  643 THR
Chi-restraints excluded: chain C residue  646 ASP
Chi-restraints excluded: chain C residue  674 HIS
Chi-restraints excluded: chain C residue  683 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 104 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 18 optimal weight:   40.0000
   chunk 100 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 114 optimal weight:    0.4980
   chunk 75 optimal weight:    1.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.266416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.238739 restraints weight = 9307.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.4657 rms_B_bonded: 1.35
r_work: 0.4195 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073   8512  Z= 0.473
  Angle     :  0.698   9.350  11685  Z= 0.344
  Chirality :  0.046   0.338   1448
  Planarity :  0.005   0.061   1568
  Dihedral  : 11.663 118.355   1617
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.24 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 24.20 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.23), residues: 1317
  helix:  1.71 (0.17), residues: 934
  sheet: -1.52 (0.55), residues: 79
  loop : -1.59 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 302 
 HIS   0.009   0.002   HIS C 518 
 PHE   0.020   0.002   PHE C 668 
 TYR   0.020   0.002   TYR B  23 
 ARG   0.004   0.001   ARG F 132 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  258 ASP cc_start: 0.7972 (p0) cc_final: 0.7650 (p0)
REVERT: C  235 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8480 (mp)
REVERT: C  578 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8527 (m-10)
REVERT: C  587 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8176 (tm-30)
  outliers start: 30
  outliers final: 22
  residues processed: 152
  average time/residue: 0.1900
  time to fit residues: 40.8493
Evaluate side-chains
  150 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain F residue   39 ASP
Chi-restraints excluded: chain F residue   84 VAL
Chi-restraints excluded: chain F residue  126 CYS
Chi-restraints excluded: chain F residue  150 TYR
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  270 LYS
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain C residue  217 ASN
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 SER
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  340 ILE
Chi-restraints excluded: chain C residue  575 VAL
Chi-restraints excluded: chain C residue  578 TYR
Chi-restraints excluded: chain C residue  587 GLU
Chi-restraints excluded: chain C residue  588 VAL
Chi-restraints excluded: chain C residue  607 GLU
Chi-restraints excluded: chain C residue  643 THR
Chi-restraints excluded: chain C residue  674 HIS
Chi-restraints excluded: chain C residue  683 ASP
Chi-restraints excluded: chain C residue  684 ILE
Chi-restraints excluded: chain C residue  705 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 57 optimal weight:    0.0670
   chunk 46 optimal weight:    7.9990
   chunk 6 optimal weight:    0.2980
   chunk 82 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 246 HIS
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 577 GLN
C 653 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4936 r_free = 0.4936 target = 0.272665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.244334 restraints weight = 9302.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.4708 rms_B_bonded: 1.60
r_work: 0.4214 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   8512  Z= 0.152
  Angle     :  0.555   9.456  11685  Z= 0.271
  Chirality :  0.041   0.306   1448
  Planarity :  0.004   0.049   1568
  Dihedral  : 10.469 119.159   1617
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.80 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 24.42 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.24), residues: 1317
  helix:  2.22 (0.17), residues: 937
  sheet: -1.57 (0.57), residues: 79
  loop : -1.51 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 555 
 HIS   0.008   0.001   HIS F 130 
 PHE   0.011   0.001   PHE C 706 
 TYR   0.014   0.001   TYR F 120 
 ARG   0.003   0.000   ARG F 285 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: F  234 TYR cc_start: 0.7765 (m-80) cc_final: 0.7236 (m-80)
REVERT: F  258 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7620 (p0)
REVERT: C  223 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7739 (mm-30)
REVERT: C  235 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8412 (mp)
REVERT: C  587 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8094 (tm-30)
  outliers start: 27
  outliers final: 17
  residues processed: 148
  average time/residue: 0.2066
  time to fit residues: 43.4760
Evaluate side-chains
  142 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   39 ASP
Chi-restraints excluded: chain F residue  126 CYS
Chi-restraints excluded: chain F residue  150 TYR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  258 ASP
Chi-restraints excluded: chain F residue  270 LYS
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain C residue  217 ASN
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 SER
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  340 ILE
Chi-restraints excluded: chain C residue  539 CYS
Chi-restraints excluded: chain C residue  587 GLU
Chi-restraints excluded: chain C residue  607 GLU
Chi-restraints excluded: chain C residue  643 THR
Chi-restraints excluded: chain C residue  646 ASP
Chi-restraints excluded: chain C residue  674 HIS
Chi-restraints excluded: chain C residue  683 ASP
Chi-restraints excluded: chain C residue  705 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 34 optimal weight:   20.0000
   chunk 7 optimal weight:   40.0000
   chunk 53 optimal weight:    1.9990
   chunk 119 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 118 optimal weight:    0.5980
   chunk 51 optimal weight:   50.0000
   chunk 11 optimal weight:   20.0000
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 257 ASN
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4915 r_free = 0.4915 target = 0.272171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.246028 restraints weight = 9499.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.4708 rms_B_bonded: 1.33
r_work: 0.4241 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3843 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8512  Z= 0.258
  Angle     :  0.575  10.149  11685  Z= 0.282
  Chirality :  0.042   0.314   1448
  Planarity :  0.004   0.046   1568
  Dihedral  :  9.780 119.953   1617
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.33 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 25.69 %
    Favored  : 69.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.24), residues: 1317
  helix:  2.36 (0.17), residues: 937
  sheet: -1.77 (0.56), residues: 81
  loop : -1.41 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 121 
 HIS   0.006   0.001   HIS F 130 
 PHE   0.018   0.001   PHE C 706 
 TYR   0.025   0.001   TYR F 120 
 ARG   0.002   0.000   ARG F 132 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: F  121 TRP cc_start: 0.5848 (t-100) cc_final: 0.5581 (t-100)
REVERT: F  234 TYR cc_start: 0.8171 (m-80) cc_final: 0.7275 (m-80)
REVERT: F  258 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7820 (p0)
REVERT: C  235 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: C  587 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8254 (tm-30)
REVERT: C  675 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8002 (pt0)
  outliers start: 25
  outliers final: 18
  residues processed: 143
  average time/residue: 0.1752
  time to fit residues: 35.9113
Evaluate side-chains
  148 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain F residue   39 ASP
Chi-restraints excluded: chain F residue   84 VAL
Chi-restraints excluded: chain F residue  126 CYS
Chi-restraints excluded: chain F residue  150 TYR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  258 ASP
Chi-restraints excluded: chain F residue  270 LYS
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  340 ILE
Chi-restraints excluded: chain C residue  539 CYS
Chi-restraints excluded: chain C residue  587 GLU
Chi-restraints excluded: chain C residue  607 GLU
Chi-restraints excluded: chain C residue  643 THR
Chi-restraints excluded: chain C residue  646 ASP
Chi-restraints excluded: chain C residue  674 HIS
Chi-restraints excluded: chain C residue  675 GLU
Chi-restraints excluded: chain C residue  683 ASP
Chi-restraints excluded: chain C residue  705 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 7 optimal weight:   40.0000
   chunk 116 optimal weight:    0.7980
   chunk 40 optimal weight:   20.0000
   chunk 23 optimal weight:    5.9990
   chunk 19 optimal weight:   50.0000
   chunk 103 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 98 optimal weight:   30.0000
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4898 r_free = 0.4898 target = 0.269525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.244914 restraints weight = 9503.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.4695 rms_B_bonded: 1.29
r_work: 0.4245 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3825 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   8512  Z= 0.397
  Angle     :  0.627  10.002  11685  Z= 0.313
  Chirality :  0.044   0.319   1448
  Planarity :  0.004   0.054   1568
  Dihedral  :  9.570 120.354   1615
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.78 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 24.84 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.24), residues: 1317
  helix:  2.22 (0.17), residues: 934
  sheet: -1.86 (0.55), residues: 81
  loop : -1.40 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 302 
 HIS   0.007   0.002   HIS C 518 
 PHE   0.019   0.002   PHE C 668 
 TYR   0.019   0.002   TYR B  23 
 ARG   0.003   0.000   ARG F 132 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   62 LYS cc_start: 0.6628 (tttt) cc_final: 0.6335 (tttt)
REVERT: F  234 TYR cc_start: 0.8366 (m-80) cc_final: 0.7366 (m-80)
REVERT: F  258 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7750 (p0)
REVERT: C  235 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8630 (mp)
REVERT: C  587 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8320 (tm-30)
REVERT: C  599 GLN cc_start: 0.7984 (mm110) cc_final: 0.7767 (mm110)
REVERT: C  675 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8044 (pt0)
  outliers start: 31
  outliers final: 22
  residues processed: 147
  average time/residue: 0.1829
  time to fit residues: 38.4622
Evaluate side-chains
  148 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain F residue   39 ASP
Chi-restraints excluded: chain F residue   84 VAL
Chi-restraints excluded: chain F residue  126 CYS
Chi-restraints excluded: chain F residue  150 TYR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  258 ASP
Chi-restraints excluded: chain F residue  270 LYS
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain F residue  284 LEU
Chi-restraints excluded: chain C residue  217 ASN
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 SER
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  340 ILE
Chi-restraints excluded: chain C residue  539 CYS
Chi-restraints excluded: chain C residue  575 VAL
Chi-restraints excluded: chain C residue  587 GLU
Chi-restraints excluded: chain C residue  607 GLU
Chi-restraints excluded: chain C residue  643 THR
Chi-restraints excluded: chain C residue  674 HIS
Chi-restraints excluded: chain C residue  675 GLU
Chi-restraints excluded: chain C residue  683 ASP
Chi-restraints excluded: chain C residue  684 ILE
Chi-restraints excluded: chain C residue  705 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 125 optimal weight:    0.7980
   chunk 111 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 24 optimal weight:   40.0000
   chunk 48 optimal weight:   50.0000
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:   30.0000
   chunk 71 optimal weight:    6.9990
   chunk 80 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.272963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.245428 restraints weight = 9531.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.4703 rms_B_bonded: 1.36
r_work: 0.4240 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8512  Z= 0.201
  Angle     :  0.535   9.312  11685  Z= 0.266
  Chirality :  0.041   0.322   1448
  Planarity :  0.004   0.043   1568
  Dihedral  :  9.172 120.744   1615
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 27.18 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.24), residues: 1317
  helix:  2.49 (0.17), residues: 936
  sheet: -1.96 (0.55), residues: 81
  loop : -1.29 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP F 121 
 HIS   0.005   0.001   HIS F 130 
 PHE   0.016   0.001   PHE C 706 
 TYR   0.018   0.001   TYR F 120 
 ARG   0.002   0.000   ARG F 116 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   62 LYS cc_start: 0.6761 (tttt) cc_final: 0.6520 (tttt)
REVERT: F  234 TYR cc_start: 0.7666 (m-80) cc_final: 0.6965 (m-80)
REVERT: F  258 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7622 (p0)
REVERT: C  235 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8397 (mp)
REVERT: C  587 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8057 (tm-30)
REVERT: C  675 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7655 (pt0)
  outliers start: 25
  outliers final: 19
  residues processed: 147
  average time/residue: 0.1802
  time to fit residues: 37.9474
Evaluate side-chains
  149 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain F residue   39 ASP
Chi-restraints excluded: chain F residue   84 VAL
Chi-restraints excluded: chain F residue  126 CYS
Chi-restraints excluded: chain F residue  150 TYR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  258 ASP
Chi-restraints excluded: chain F residue  270 LYS
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 SER
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  340 ILE
Chi-restraints excluded: chain C residue  539 CYS
Chi-restraints excluded: chain C residue  587 GLU
Chi-restraints excluded: chain C residue  588 VAL
Chi-restraints excluded: chain C residue  607 GLU
Chi-restraints excluded: chain C residue  643 THR
Chi-restraints excluded: chain C residue  674 HIS
Chi-restraints excluded: chain C residue  675 GLU
Chi-restraints excluded: chain C residue  683 ASP
Chi-restraints excluded: chain C residue  705 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 117 optimal weight:    0.1980
   chunk 93 optimal weight:    0.8980
   chunk 97 optimal weight:   30.0000
   chunk 102 optimal weight:   30.0000
   chunk 77 optimal weight:   20.0000
   chunk 90 optimal weight:    0.0670
   chunk 39 optimal weight:   40.0000
   chunk 16 optimal weight:   20.0000
   chunk 71 optimal weight:    5.9990
   chunk 18 optimal weight:   40.0000
   chunk 127 optimal weight:    0.9980
   overall best weight:    1.6320

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

Flipped N/Q/H residues before XYZ refinement:
** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 599 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4898 r_free = 0.4898 target = 0.269874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.243929 restraints weight = 9519.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.4691 rms_B_bonded: 1.40
r_work: 0.4217 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work (final): 0.4217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   8512  Z= 0.350
  Angle     :  0.607   9.318  11685  Z= 0.304
  Chirality :  0.043   0.337   1448
  Planarity :  0.004   0.053   1568
  Dihedral  :  9.181 121.309   1615
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 26.75 %
    Favored  : 67.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.24), residues: 1317
  helix:  2.38 (0.17), residues: 934
  sheet: -1.98 (0.54), residues: 81
  loop : -1.31 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F 121 
 HIS   0.006   0.001   HIS C 518 
 PHE   0.022   0.002   PHE C 706 
 TYR   0.020   0.002   TYR C 571 
 ARG   0.002   0.000   ARG F 132 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   62 LYS cc_start: 0.6764 (tttt) cc_final: 0.6527 (tttt)
REVERT: F  234 TYR cc_start: 0.7745 (m-80) cc_final: 0.7022 (m-80)
REVERT: F  258 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7652 (p0)
REVERT: C  235 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8431 (mp)
REVERT: C  587 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8087 (tm-30)
  outliers start: 26
  outliers final: 21
  residues processed: 144
  average time/residue: 0.1708
  time to fit residues: 35.5049
Evaluate side-chains
  149 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain F residue   39 ASP
Chi-restraints excluded: chain F residue   84 VAL
Chi-restraints excluded: chain F residue  126 CYS
Chi-restraints excluded: chain F residue  150 TYR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  258 ASP
Chi-restraints excluded: chain F residue  270 LYS
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 SER
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  340 ILE
Chi-restraints excluded: chain C residue  539 CYS
Chi-restraints excluded: chain C residue  575 VAL
Chi-restraints excluded: chain C residue  587 GLU
Chi-restraints excluded: chain C residue  588 VAL
Chi-restraints excluded: chain C residue  607 GLU
Chi-restraints excluded: chain C residue  643 THR
Chi-restraints excluded: chain C residue  674 HIS
Chi-restraints excluded: chain C residue  675 GLU
Chi-restraints excluded: chain C residue  683 ASP
Chi-restraints excluded: chain C residue  705 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 99 optimal weight:   30.0000
   chunk 40 optimal weight:   20.0000
   chunk 97 optimal weight:   40.0000
   chunk 55 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0470
   chunk 124 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:   60.0000
   chunk 122 optimal weight:    0.6980
   chunk 78 optimal weight:   10.0000
   chunk 105 optimal weight:    9.9990
   overall best weight:    1.1080

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

Flipped N/Q/H residues before XYZ refinement:
** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.271592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.246265 restraints weight = 9441.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.4710 rms_B_bonded: 1.30
r_work: 0.4235 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8512  Z= 0.254
  Angle     :  0.555   9.311  11685  Z= 0.278
  Chirality :  0.041   0.343   1448
  Planarity :  0.004   0.042   1568
  Dihedral  :  8.992 121.584   1615
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 27.39 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.24), residues: 1317
  helix:  2.48 (0.17), residues: 938
  sheet: -1.97 (0.55), residues: 81
  loop : -1.25 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F 121 
 HIS   0.005   0.001   HIS C 518 
 PHE   0.025   0.001   PHE C 706 
 TYR   0.017   0.001   TYR C 234 
 ARG   0.002   0.000   ARG F 285 

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   62 LYS cc_start: 0.6934 (tttt) cc_final: 0.6692 (tttt)
REVERT: F  234 TYR cc_start: 0.7651 (m-80) cc_final: 0.6950 (m-80)
REVERT: F  258 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7648 (p0)
REVERT: C  235 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8413 (mp)
REVERT: C  587 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8086 (tm-30)
REVERT: C  684 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.6960 (mp)
  outliers start: 24
  outliers final: 20
  residues processed: 142
  average time/residue: 0.2011
  time to fit residues: 41.3828
Evaluate side-chains
  147 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 1.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain F residue   39 ASP
Chi-restraints excluded: chain F residue   84 VAL
Chi-restraints excluded: chain F residue  126 CYS
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  258 ASP
Chi-restraints excluded: chain F residue  270 LYS
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 SER
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  340 ILE
Chi-restraints excluded: chain C residue  539 CYS
Chi-restraints excluded: chain C residue  575 VAL
Chi-restraints excluded: chain C residue  587 GLU
Chi-restraints excluded: chain C residue  588 VAL
Chi-restraints excluded: chain C residue  607 GLU
Chi-restraints excluded: chain C residue  643 THR
Chi-restraints excluded: chain C residue  674 HIS
Chi-restraints excluded: chain C residue  675 GLU
Chi-restraints excluded: chain C residue  683 ASP
Chi-restraints excluded: chain C residue  684 ILE
Chi-restraints excluded: chain C residue  705 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 112 optimal weight:    0.8980
   chunk 0 optimal weight:   60.0000
   chunk 47 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0980
   chunk 96 optimal weight:    8.9990
   chunk 58 optimal weight:   40.0000
   chunk 36 optimal weight:   30.0000
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.270289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.245560 restraints weight = 9567.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.4703 rms_B_bonded: 1.25
r_work: 0.4237 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8512  Z= 0.307
  Angle     :  0.576   9.351  11685  Z= 0.290
  Chirality :  0.042   0.357   1448
  Planarity :  0.004   0.043   1568
  Dihedral  :  8.926 121.871   1615
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 27.39 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.24), residues: 1317
  helix:  2.45 (0.17), residues: 937
  sheet: -2.01 (0.54), residues: 81
  loop : -1.25 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP F 121 
 HIS   0.005   0.001   HIS C 674 
 PHE   0.024   0.002   PHE C 706 
 TYR   0.016   0.001   TYR F 120 
 ARG   0.002   0.000   ARG F 285 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4735.49 seconds
wall clock time: 84 minutes 53.60 seconds (5093.60 seconds total)