Starting phenix.real_space_refine
on Thu Jun 12 17:24:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y1p_38842/06_2025/8y1p_38842.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y1p_38842/06_2025/8y1p_38842.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y1p_38842/06_2025/8y1p_38842.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y1p_38842/06_2025/8y1p_38842.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y1p_38842/06_2025/8y1p_38842.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y1p_38842/06_2025/8y1p_38842.cif"
  }
  resolution = 3.45
  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=  -0.002 sd=   0.092
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      65      5.16       5
     C    9071      2.51       5
     N    2451      2.21       5
     O    2452      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 93 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14041
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 13933
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1800, 13925
          Classifications: {'peptide': 1800}
          Link IDs: {'PTRANS': 111, 'TRANS': 1688}
          Chain breaks: 9
      Conformer: "B"
        Number of residues, atoms: 1800, 13925
          Classifications: {'peptide': 1800}
          Link IDs: {'PTRANS': 111, 'TRANS': 1688}
          Chain breaks: 9
          bond proxies already assigned to first conformer: 14257
    Chain: "A"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 108
          Unusual residues: {'17F': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ALEU A1881 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CD2BLEU A1881 " occ=0.50
  Time building chain proxies: 14.04, per 1000 atoms: 1.00
  Number of scatterers: 14041
  At special positions: 0
  Unit cell: (80.25, 108.07, 214, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      65     16.00
     P       2     15.00
     O    2452      8.00
     N    2451      7.00
     C    9071      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  81 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 225 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 267 " - pdb=" SG  CYS A 406 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 536 " - pdb=" SG  CYS A1347 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A1345 " - pdb=" SG  CYS A1359 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM13983  O6  17F A2201 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.50
  Conformation dependent library (CDL) restraints added in 3.5 seconds
  

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3304

  Finding SS restraints...
    Secondary structure from input PDB file:
      86 helices and 10 sheets defined
      51.5% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 20
      removed outlier: 4.623A  pdb=" N   MET A   8 " --> pdb=" O   TRP A   4 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ASN A  14 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 31
      removed outlier: 3.681A  pdb=" N   VAL A  27 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 34
      No H-bonds generated for 'chain 'A' and resid 32 through 34'
    Processing helix  chain 'A' and resid 38 through 44
    Processing helix  chain 'A' and resid 62 through 65
      removed outlier: 3.517A  pdb=" N   GLY A  65 " --> pdb=" O   PRO A  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 62 through 65'
    Processing helix  chain 'A' and resid 66 through 75
    Processing helix  chain 'A' and resid 100 through 114
    Processing helix  chain 'A' and resid 115 through 126
      removed outlier: 3.791A  pdb=" N   HIS A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG A 120 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 194
      removed outlier: 4.043A  pdb=" N   GLN A 192 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLU A 193 " --> pdb=" O   ASP A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 208
    Processing helix  chain 'A' and resid 219 through 224
      removed outlier: 4.072A  pdb=" N   ALA A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 275
      removed outlier: 4.030A  pdb=" N   GLU A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LEU A 270 " --> pdb=" O   ALA A 266 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 292
      removed outlier: 4.596A  pdb=" N   ARG A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 301 through 317
      removed outlier: 4.328A  pdb=" N   GLN A 310 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   THR A 314 " --> pdb=" O   GLN A 310 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   PHE A 315 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLU A 317 " --> pdb=" O   ARG A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
      removed outlier: 3.885A  pdb=" N   LEU A 321 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 318 through 321'
    Processing helix  chain 'A' and resid 322 through 337
      removed outlier: 3.741A  pdb=" N   GLU A 326 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 347 through 352
    Processing helix  chain 'A' and resid 377 through 383
      removed outlier: 3.818A  pdb=" N   GLY A 383 " --> pdb=" O   PRO A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.873A  pdb=" N   THR A 399 " --> pdb=" O   HIS A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 430
      removed outlier: 3.825A  pdb=" N   SER A 423 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ALA A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 501
      removed outlier: 3.565A  pdb=" N   TRP A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 520
      removed outlier: 3.812A  pdb=" N   ASP A 508 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   LEU A 509 " --> pdb=" O   TYR A 505 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ARG A 512 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER A 519 " --> pdb=" O   VAL A 515 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY A 520 " --> pdb=" O   ARG A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 545
      removed outlier: 3.590A  pdb=" N   VAL A 545 " --> pdb=" O   VAL A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 556
    Processing helix  chain 'A' and resid 558 through 575
      removed outlier: 3.583A  pdb=" N   THR A 563 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS A 573 " --> pdb=" O   VAL A 569 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A 575 " --> pdb=" O   ARG A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 583
    Processing helix  chain 'A' and resid 588 through 600
      removed outlier: 3.618A  pdb=" N   TRP A 592 " --> pdb=" O   ARG A 588 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TRP A 595 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER A 598 " --> pdb=" O   GLY A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 606
    Processing helix  chain 'A' and resid 610 through 617
    Processing helix  chain 'A' and resid 624 through 633
      removed outlier: 3.569A  pdb=" N   VAL A 628 " --> pdb=" O   HIS A 624 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   PHE A 631 " --> pdb=" O   VAL A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 644
    Processing helix  chain 'A' and resid 645 through 648
    Processing helix  chain 'A' and resid 656 through 666
      removed outlier: 3.893A  pdb=" N   GLY A 661 " --> pdb=" O   ALA A 657 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   LEU A 662 " --> pdb=" O   ALA A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 676
      removed outlier: 3.501A  pdb=" N   VAL A 672 " --> pdb=" O   TYR A 668 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   CYS A 674 " --> pdb=" O   PRO A 670 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 676 " --> pdb=" O   VAL A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 697
    Processing helix  chain 'A' and resid 697 through 705
      removed outlier: 4.073A  pdb=" N   SER A 703 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 743
      removed outlier: 3.785A  pdb=" N   VAL A 733 " --> pdb=" O   SER A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 755
      removed outlier: 5.658A  pdb=" N   ALA A 753 " --> pdb=" O   TRP A 749 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL A 754 " --> pdb=" O   TYR A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 855
      removed outlier: 3.731A  pdb=" N   THR A 850 " --> pdb=" O   GLY A 846 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 851 " --> pdb=" O   LYS A 847 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER A 852 " --> pdb=" O   THR A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 875 through 880
      removed outlier: 4.221A  pdb=" N   ILE A 879 " --> pdb=" O   SER A 875 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 908
      removed outlier: 3.609A  pdb=" N   VAL A 902 " --> pdb=" O   VAL A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 927
      removed outlier: 3.696A  pdb=" N   GLN A 920 " --> pdb=" O   VAL A 916 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ASP A 921 " --> pdb=" O   GLY A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 943 through 949
    Processing helix  chain 'A' and resid 950 through 954
      removed outlier: 3.859A  pdb=" N   ALA A 953 " --> pdb=" O   VAL A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 985
    Processing helix  chain 'A' and resid 997 through 1004
      removed outlier: 4.093A  pdb=" N   ALA A1001 " --> pdb=" O   HIS A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1021 through 1030
    Processing helix  chain 'A' and resid 1074 through 1083
      removed outlier: 4.033A  pdb=" N   LEU A1078 " --> pdb=" O   GLY A1074 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1107 through 1111
      removed outlier: 3.856A  pdb=" N   ASP A1110 " --> pdb=" O   GLY A1107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1113 through 1122
      removed outlier: 3.542A  pdb=" N   THR A1122 " --> pdb=" O   ARG A1118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1138 through 1151
      removed outlier: 3.679A  pdb=" N   ILE A1142 " --> pdb=" O   SER A1138 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU A1149 " --> pdb=" O   LYS A1145 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   CYS A1150 " --> pdb=" O   VAL A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1220 through 1235
      removed outlier: 4.059A  pdb=" N   LEU A1224 " --> pdb=" O   GLN A1220 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LYS A1227 " --> pdb=" O   ALA A1223 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER A1235 " --> pdb=" O   LEU A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1243 through 1257
      removed outlier: 4.070A  pdb=" N   ALA A1247 " --> pdb=" O   ILE A1243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1292 through 1305
      removed outlier: 3.539A  pdb=" N   LEU A1296 " --> pdb=" O   GLY A1292 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A1297 " --> pdb=" O   ARG A1293 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLU A1298 " --> pdb=" O   ALA A1294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1324 through 1332
    Processing helix  chain 'A' and resid 1386 through 1394
      removed outlier: 3.743A  pdb=" N   LEU A1391 " --> pdb=" O   LEU A1387 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   VAL A1392 " --> pdb=" O   SER A1388 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS A1393 " --> pdb=" O   ASP A1389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1394 through 1399
      removed outlier: 3.511A  pdb=" N   LEU A1398 " --> pdb=" O   THR A1394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1400 through 1404
      removed outlier: 3.839A  pdb=" N   LYS A1404 " --> pdb=" O   GLN A1401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1430 through 1440
    Processing helix  chain 'A' and resid 1451 through 1464
      removed outlier: 3.951A  pdb=" N   LEU A1455 " --> pdb=" O   LEU A1451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1477 through 1480
      removed outlier: 3.594A  pdb=" N   TRP A1480 " --> pdb=" O   ASN A1477 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1477 through 1480'
    Processing helix  chain 'A' and resid 1481 through 1496
    Processing helix  chain 'A' and resid 1520 through 1532
      removed outlier: 3.758A  pdb=" N   GLU A1526 " --> pdb=" O   GLU A1522 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLY A1527 " --> pdb=" O   GLN A1523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1533 through 1549
      removed outlier: 4.203A  pdb=" N   VAL A1549 " --> pdb=" O   ALA A1545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1549 through 1559
      removed outlier: 3.960A  pdb=" N   LEU A1555 " --> pdb=" O   ALA A1551 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   VAL A1556 " --> pdb=" O   SER A1552 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   LEU A1557 " --> pdb=" O   PHE A1553 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLU A1559 " --> pdb=" O   LEU A1555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1575 through 1605
      removed outlier: 4.536A  pdb=" N   TYR A1579 " --> pdb=" O   SER A1575 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LEU A1581 " --> pdb=" O   THR A1577 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   PHE A1584 " --> pdb=" O   TRP A1580 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   VAL A1593 " --> pdb=" O   CYS A1589 " (cutoff:3.500A)
      Proline residue:  A1594  - end of helix
      removed outlier: 4.195A  pdb=" N   VAL A1598 " --> pdb=" O   PRO A1594 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ILE A1601 " --> pdb=" O   ILE A1597 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   PHE A1602 " --> pdb=" O   VAL A1598 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LEU A1603 " --> pdb=" O   VAL A1599 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE A1605 " --> pdb=" O   ILE A1601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1618 through 1631
      removed outlier: 5.080A  pdb=" N   GLY A1627 " --> pdb=" O   LEU A1623 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   TRP A1628 " --> pdb=" O   LEU A1624 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR A1631 " --> pdb=" O   GLY A1627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1632 through 1638
      removed outlier: 3.715A  pdb=" N   TYR A1635 " --> pdb=" O   PRO A1632 " (cutoff:3.500A)
      Proline residue:  A1636  - end of helix
      No H-bonds generated for 'chain 'A' and resid 1632 through 1638'
    Processing helix  chain 'A' and resid 1647 through 1667
      removed outlier: 4.091A  pdb=" N   THR A1666 " --> pdb=" O   GLY A1662 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   PHE A1667 " --> pdb=" O   SER A1663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1677 through 1689
      removed outlier: 3.563A  pdb=" N   PHE A1688 " --> pdb=" O   LEU A1684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1697 through 1719
      removed outlier: 4.677A  pdb=" N   MET A1703 " --> pdb=" O   GLY A1699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1732 through 1740
    Processing helix  chain 'A' and resid 1742 through 1755
      removed outlier: 3.699A  pdb=" N   HIS A1753 " --> pdb=" O   LEU A1749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1833 through 1842
    Processing helix  chain 'A' and resid 1861 through 1868
    Processing helix  chain 'A' and resid 1884 through 1893
      removed outlier: 4.000A  pdb=" N   LEU A1888 " --> pdb=" O   GLY A1884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1900 through 1913
      removed outlier: 3.668A  pdb=" N   GLN A1904 " --> pdb=" O   ALA A1900 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A1913 " --> pdb=" O   GLY A1909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1914 through 1917
      removed outlier: 4.001A  pdb=" N   TRP A1917 " --> pdb=" O   GLY A1914 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1914 through 1917'
    Processing helix  chain 'A' and resid 1928 through 1940
    Processing helix  chain 'A' and resid 1957 through 1972
      removed outlier: 3.977A  pdb=" N   ARG A1961 " --> pdb=" O   ASP A1957 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   PHE A1963 " --> pdb=" O   SER A1959 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   LEU A1969 " --> pdb=" O   TRP A1965 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL A1972 " --> pdb=" O   LEU A1968 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1985 through 1991
      removed outlier: 3.731A  pdb=" N   LEU A1991 " --> pdb=" O   GLU A1987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2008 through 2016
    Processing helix  chain 'A' and resid 2027 through 2042
      removed outlier: 4.666A  pdb=" N   GLN A2032 " --> pdb=" O   ALA A2028 " (cutoff:3.500A)
      Proline residue:  A2033  - end of helix
    Processing helix  chain 'A' and resid 2062 through 2066
    Processing helix  chain 'A' and resid 2069 through 2077
    Processing helix  chain 'A' and resid 2096 through 2102
      removed outlier: 3.955A  pdb=" N   PHE A2100 " --> pdb=" O   VAL A2096 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60
      removed outlier: 6.672A  pdb=" N   TYR A 528 " --> pdb=" O   ILE A1473 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   PHE A1475 " --> pdb=" O   TYR A 528 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   GLN A 530 " --> pdb=" O   PHE A1475 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414
      removed outlier: 6.872A  pdb=" N   LYS A 294 " --> pdb=" O   TRP A 435 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLY A 437 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   LEU A 296 " --> pdb=" O   GLY A 437 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL A 462 " --> pdb=" O   THR A1511 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   LEU A1513 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   ILE A 464 " --> pdb=" O   LEU A1513 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 960 through 961
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1010 through 1012
      removed outlier: 5.436A  pdb=" N   ALA A1012 " --> pdb=" O   LEU A1016 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   LEU A1016 " --> pdb=" O   ALA A1012 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1090 through 1094
      removed outlier: 7.124A  pdb=" N   VAL A1100 " --> pdb=" O   VAL A1092 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU A1099 " --> pdb=" O   LEU A1037 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   LEU A1035 " --> pdb=" O   LEU A1101 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1279 through 1283
      removed outlier: 3.510A  pdb=" N   GLN A1380 " --> pdb=" O   SER A1281 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1793 through 1794
      removed outlier: 3.558A  pdb=" N   LEU A1793 " --> pdb=" O   ILE A1817 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE A1817 " --> pdb=" O   LEU A1793 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1824 through 1825
      removed outlier: 7.292A  pdb=" N   GLY A1824 " --> pdb=" O   ALA A1996 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2046 through 2051
      removed outlier: 4.969A  pdb=" N   LEU A2047 " --> pdb=" O   GLN A2058 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   GLN A2058 " --> pdb=" O   LEU A2047 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU A2049 " --> pdb=" O   ARG A2056 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ARG A2025 " --> pdb=" O   ASP A2085 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   ASP A2085 " --> pdb=" O   ARG A2025 " (cutoff:3.500A)

    511 hydrogen bonds defined for protein.
    1485 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: 5.16

  Time building geometry restraints manager: 4.11 seconds

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

  Histogram of bond lengths:
        1.20 -     1.34: 4451
        1.34 -     1.48: 3980
        1.48 -     1.61: 5852
        1.61 -     1.75: 7
        1.75 -     1.89: 91
  Bond restraints: 14381
  Sorted by residual:
  bond pdb=" C17 17F A2202 "
       pdb=" O9  17F A2202 "
    ideal  model  delta    sigma   weight residual
    1.330  1.454 -0.124 2.00e-02 2.50e+03 3.85e+01
  bond pdb=" C17 17F A2201 "
       pdb=" O9  17F A2201 "
    ideal  model  delta    sigma   weight residual
    1.330  1.453 -0.123 2.00e-02 2.50e+03 3.81e+01
  bond pdb=" C7  17F A2202 "
       pdb=" O7  17F A2202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.454 -0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" C7  17F A2201 "
       pdb=" O7  17F A2201 "
    ideal  model  delta    sigma   weight residual
    1.335  1.454 -0.119 2.00e-02 2.50e+03 3.53e+01
  bond pdb=" O2  17F A2202 "
       pdb=" P1  17F A2202 "
    ideal  model  delta    sigma   weight residual
    1.498  1.610 -0.112 2.00e-02 2.50e+03 3.15e+01
  ... (remaining 14376 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.80: 18962
        3.80 -     7.61: 476
        7.61 -    11.41: 76
       11.41 -    15.22: 22
       15.22 -    19.02: 2
  Bond angle restraints: 19538
  Sorted by residual:
  angle pdb=" CA  TYR A 744 "
        pdb=" CB  TYR A 744 "
        pdb=" CG  TYR A 744 "
      ideal   model   delta    sigma   weight residual
     113.90  127.05  -13.15 1.80e+00 3.09e-01 5.34e+01
  angle pdb=" CA  CYS A  81 "
        pdb=" CB  CYS A  81 "
        pdb=" SG  CYS A  81 "
      ideal   model   delta    sigma   weight residual
     114.40  129.87  -15.47 2.30e+00 1.89e-01 4.53e+01
  angle pdb=" CB  MET A1275 "
        pdb=" CG  MET A1275 "
        pdb=" SD  MET A1275 "
      ideal   model   delta    sigma   weight residual
     112.70  131.72  -19.02 3.00e+00 1.11e-01 4.02e+01
  angle pdb=" CA  CYS A 536 "
        pdb=" CB  CYS A 536 "
        pdb=" SG  CYS A 536 "
      ideal   model   delta    sigma   weight residual
     114.40  128.58  -14.18 2.30e+00 1.89e-01 3.80e+01
  angle pdb=" CA  GLU A 572 "
        pdb=" CB  GLU A 572 "
        pdb=" CG  GLU A 572 "
      ideal   model   delta    sigma   weight residual
     114.10  124.26  -10.16 2.00e+00 2.50e-01 2.58e+01
  ... (remaining 19533 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.65: 8348
       33.65 -    67.30: 212
       67.30 -   100.95: 20
      100.95 -   134.61: 1
      134.61 -   168.26: 1
  Dihedral angle restraints: 8582
    sinusoidal: 3449
      harmonic: 5133
  Sorted by residual:
  dihedral pdb=" CB  CYS A  54 "
           pdb=" SG  CYS A  54 "
           pdb=" SG  CYS A  81 "
           pdb=" CB  CYS A  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   10.73   82.27     1      1.00e+01 1.00e-02 8.31e+01
  dihedral pdb=" CA  THR A1274 "
           pdb=" C   THR A1274 "
           pdb=" N   MET A1275 "
           pdb=" CA  MET A1275 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.83  -28.17     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  GLY A 863 "
           pdb=" C   GLY A 863 "
           pdb=" N   SER A 864 "
           pdb=" CA  SER A 864 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.84  -28.16     0      5.00e+00 4.00e-02 3.17e+01
  ... (remaining 8579 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1811
       0.090 -    0.180: 345
       0.180 -    0.271: 46
       0.271 -    0.361: 5
       0.361 -    0.451: 8
  Chirality restraints: 2215
  Sorted by residual:
  chirality pdb=" CB  VAL A 719 "
            pdb=" CA  VAL A 719 "
            pdb=" CG1 VAL A 719 "
            pdb=" CG2 VAL A 719 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.18   -0.45 2.00e-01 2.50e+01 5.08e+00
  chirality pdb=" CB  ILE A 836 "
            pdb=" CA  ILE A 836 "
            pdb=" CG1 ILE A 836 "
            pdb=" CG2 ILE A 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.44 2.00e-01 2.50e+01 4.77e+00
  chirality pdb=" CB  VAL A 504 "
            pdb=" CA  VAL A 504 "
            pdb=" CG1 VAL A 504 "
            pdb=" CG2 VAL A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.20   -0.43 2.00e-01 2.50e+01 4.71e+00
  ... (remaining 2212 not shown)

  Planarity restraints: 2497
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 415 "    0.100 5.00e-02 4.00e+02   1.51e-01 3.66e+01
        pdb=" N   PRO A 416 "   -0.262 5.00e-02 4.00e+02
        pdb=" CA  PRO A 416 "    0.082 5.00e-02 4.00e+02
        pdb=" CD  PRO A 416 "    0.080 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 744 "    0.060 2.00e-02 2.50e+03   4.27e-02 3.65e+01
        pdb=" CG  TYR A 744 "   -0.102 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 744 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 744 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 744 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 744 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 744 "    0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 744 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A1265 "   -0.025 2.00e-02 2.50e+03   4.92e-02 2.42e+01
        pdb=" C   HIS A1265 "    0.085 2.00e-02 2.50e+03
        pdb=" O   HIS A1265 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   TYR A1266 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 2494 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 223
        2.65 -     3.21: 11865
        3.21 -     3.77: 20910
        3.77 -     4.34: 26769
        4.34 -     4.90: 45131
  Nonbonded interactions: 104898
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A  24 "
            pdb=" O6  17F A2201 "
     model   vdw
     2.087 3.120
  nonbonded pdb=" OH  TYR A1276 "
            pdb=" O   GLY A1479 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OD2 ASP A1587 "
            pdb=" OH  TYR A1635 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OE1 GLN A 642 "
            pdb=" OH  TYR A 744 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   LEU A 290 "
            pdb=" NZ  LYS A 411 "
     model   vdw
     2.322 3.120
  ... (remaining 104893 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     42.380
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
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      :  0.016   0.736  14387  Z= 0.851
  Angle     :  1.488  19.023  19548  Z= 0.734
  Chirality :  0.076   0.451   2215
  Planarity :  0.011   0.151   2497
  Dihedral  : 15.635 168.257   5263
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.46 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  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: -4.54 (0.16), residues: 1783
  helix: -3.04 (0.13), residues: 895
  sheet: -2.79 (0.38), residues: 156
  loop : -2.81 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP A1336 
 HIS   0.018   0.003   HIS A1508 
 PHE   0.046   0.004   PHE A 297 
 TYR   0.102   0.004   TYR A 744 
 ARG   0.028   0.004   ARG A1349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16421 (  511)
  hydrogen bonds       : angle       7.39944 ( 1485)
  SS BOND              : bond        0.02116 (    5)
  SS BOND              : angle       4.26564 (   10)
  covalent geometry    : bond        0.01441 (14381)
  covalent geometry    : angle       1.48541 (19538)
  Misc. bond           : bond        0.73642 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
REVERT: A 1275 MET cc_start: 0.7134 (ptp) cc_final: 0.6855 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.2378
  time to fit residues: 36.0916
Evaluate side-chains
  87 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 151 optimal weight:   10.0000
   chunk 136 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 92 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 141 optimal weight:    9.9990
   chunk 54 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   chunk 163 optimal weight:   20.0000
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 119 HIS
A1077 GLN
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1488 ASN
** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.230913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.184217 restraints weight = 30223.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 3.81
r_work: 0.3154 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14387  Z= 0.185
  Angle     :  0.790  10.942  19548  Z= 0.387
  Chirality :  0.045   0.268   2215
  Planarity :  0.007   0.104   2497
  Dihedral  : 10.738 164.582   2055
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  5.15 %
    Favored  : 94.51 %
  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: -3.55 (0.18), residues: 1783
  helix: -2.00 (0.15), residues: 896
  sheet: -2.53 (0.39), residues: 149
  loop : -2.63 (0.21), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 500 
 HIS   0.011   0.001   HIS A 119 
 PHE   0.027   0.002   PHE A1240 
 TYR   0.039   0.002   TYR A 744 
 ARG   0.005   0.000   ARG A1838 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04362 (  511)
  hydrogen bonds       : angle       5.32389 ( 1485)
  SS BOND              : bond        0.00782 (    5)
  SS BOND              : angle       2.07576 (   10)
  covalent geometry    : bond        0.00445 (14381)
  covalent geometry    : angle       0.78836 (19538)
  Misc. bond           : bond        0.00058 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 MET cc_start: 0.7622 (tmm) cc_final: 0.7262 (tmm)
REVERT: A  522 ASN cc_start: 0.9097 (t0) cc_final: 0.8668 (p0)
REVERT: A 1275 MET cc_start: 0.7112 (ptp) cc_final: 0.6676 (ptp)
  outliers start: 5
  outliers final: 2
  residues processed: 103
  average time/residue: 0.2345
  time to fit residues: 38.5947
Evaluate side-chains
  91 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue 1284 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 112 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 79 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 160 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 163 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
A 181 HIS
A 766 ASN
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.230862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.184911 restraints weight = 30035.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.4058 rms_B_bonded: 3.76
r_work: 0.3159 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14387  Z= 0.172
  Angle     :  0.743  10.389  19548  Z= 0.359
  Chirality :  0.044   0.268   2215
  Planarity :  0.006   0.079   2497
  Dihedral  : 10.012 162.013   2055
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  8.20 %
    Favored  : 91.33 %
  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: -3.06 (0.19), residues: 1783
  helix: -1.51 (0.16), residues: 891
  sheet: -2.25 (0.41), residues: 149
  loop : -2.54 (0.22), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 500 
 HIS   0.018   0.001   HIS A 119 
 PHE   0.025   0.001   PHE A1240 
 TYR   0.035   0.002   TYR A 744 
 ARG   0.005   0.000   ARG A1705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04043 (  511)
  hydrogen bonds       : angle       4.93504 ( 1485)
  SS BOND              : bond        0.00826 (    5)
  SS BOND              : angle       2.12229 (   10)
  covalent geometry    : bond        0.00415 (14381)
  covalent geometry    : angle       0.74162 (19538)
  Misc. bond           : bond        0.00303 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 1.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 MET cc_start: 0.7586 (tmm) cc_final: 0.7323 (tmm)
REVERT: A  522 ASN cc_start: 0.9064 (t0) cc_final: 0.8760 (p0)
REVERT: A  965 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8059 (tm-30)
REVERT: A 1275 MET cc_start: 0.7280 (ptp) cc_final: 0.6495 (ptp)
  outliers start: 7
  outliers final: 4
  residues processed: 103
  average time/residue: 0.2412
  time to fit residues: 40.0952
Evaluate side-chains
  100 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue 1284 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 87 optimal weight:   50.0000
   chunk 19 optimal weight:    0.9980
   chunk 119 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 152 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0270
   chunk 76 optimal weight:    0.3980
   overall best weight:    1.0842

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
A 181 HIS
A 642 GLN
A 766 ASN
** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 HIS
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.231413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.185063 restraints weight = 35064.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 4.05
r_work: 0.3131 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3085
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3085
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14387  Z= 0.149
  Angle     :  0.702   9.986  19548  Z= 0.337
  Chirality :  0.043   0.257   2215
  Planarity :  0.005   0.068   2497
  Dihedral  :  9.535 161.943   2055
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.06 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 10.23 %
    Favored  : 89.30 %
  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: -2.69 (0.19), residues: 1783
  helix: -1.17 (0.17), residues: 886
  sheet: -2.07 (0.42), residues: 149
  loop : -2.40 (0.22), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A   4 
 HIS   0.012   0.001   HIS A 119 
 PHE   0.022   0.001   PHE A1240 
 TYR   0.027   0.001   TYR A 744 
 ARG   0.005   0.000   ARG A1705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  511)
  hydrogen bonds       : angle       4.71131 ( 1485)
  SS BOND              : bond        0.00691 (    5)
  SS BOND              : angle       1.86104 (   10)
  covalent geometry    : bond        0.00358 (14381)
  covalent geometry    : angle       0.70064 (19538)
  Misc. bond           : bond        0.00219 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 MET cc_start: 0.7653 (tmm) cc_final: 0.7123 (tmm)
REVERT: A  522 ASN cc_start: 0.8989 (t0) cc_final: 0.8767 (p0)
REVERT: A  965 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8215 (tm-30)
REVERT: A 1275 MET cc_start: 0.7178 (ptp) cc_final: 0.6039 (ptp)
  outliers start: 7
  outliers final: 6
  residues processed: 110
  average time/residue: 0.2399
  time to fit residues: 41.7986
Evaluate side-chains
  100 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 1.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue  181 HIS
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue 1284 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 62 optimal weight:    0.4980
   chunk 110 optimal weight:    3.9990
   chunk 13 optimal weight:   50.0000
   chunk 136 optimal weight:    7.9990
   chunk 159 optimal weight:    8.9990
   chunk 35 optimal weight:    0.8980
   chunk 95 optimal weight:   20.0000
   chunk 163 optimal weight:   50.0000
   chunk 56 optimal weight:    0.5980
   chunk 157 optimal weight:    6.9990
   overall best weight:    2.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
A 181 HIS
A 766 ASN
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.233513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.189475 restraints weight = 26271.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.4142 rms_B_bonded: 3.45
r_work: 0.3687 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  14387  Z= 0.280
  Angle     :  0.792  11.152  19548  Z= 0.383
  Chirality :  0.048   0.260   2215
  Planarity :  0.006   0.064   2497
  Dihedral  :  9.724 158.795   2055
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.01 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.92 %
    Favored  : 87.20 %
  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: -2.72 (0.19), residues: 1783
  helix: -1.17 (0.17), residues: 889
  sheet: -2.15 (0.42), residues: 149
  loop : -2.43 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 500 
 HIS   0.022   0.002   HIS A 181 
 PHE   0.028   0.002   PHE A1486 
 TYR   0.040   0.002   TYR A 744 
 ARG   0.004   0.000   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04322 (  511)
  hydrogen bonds       : angle       4.78371 ( 1485)
  SS BOND              : bond        0.01138 (    5)
  SS BOND              : angle       2.69702 (   10)
  covalent geometry    : bond        0.00688 (14381)
  covalent geometry    : angle       0.78979 (19538)
  Misc. bond           : bond        0.00202 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  522 ASN cc_start: 0.9071 (t0) cc_final: 0.8758 (p0)
REVERT: A 1275 MET cc_start: 0.7091 (ptp) cc_final: 0.6489 (ptp)
REVERT: A 1839 MET cc_start: 0.3080 (ptp) cc_final: 0.2786 (ptp)
  outliers start: 13
  outliers final: 9
  residues processed: 103
  average time/residue: 0.2277
  time to fit residues: 37.4226
Evaluate side-chains
  100 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  744 TYR
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1336 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 87 optimal weight:   50.0000
   chunk 133 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 153 optimal weight:    8.9990
   chunk 137 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 119 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 138 optimal weight:   10.0000
   chunk 120 optimal weight:    1.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
A 766 ASN
** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.235084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.193205 restraints weight = 32027.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.4181 rms_B_bonded: 3.50
r_work: 0.3689 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  14387  Z= 0.187
  Angle     :  0.714  10.602  19548  Z= 0.344
  Chirality :  0.044   0.250   2215
  Planarity :  0.005   0.062   2497
  Dihedral  :  9.395 161.282   2055
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 12.94 %
    Favored  : 86.38 %
  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: -2.49 (0.20), residues: 1783
  helix: -0.98 (0.17), residues: 889
  sheet: -1.95 (0.43), residues: 149
  loop : -2.35 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 500 
 HIS   0.004   0.001   HIS A1508 
 PHE   0.021   0.001   PHE A1486 
 TYR   0.032   0.002   TYR A 744 
 ARG   0.008   0.000   ARG A1434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  511)
  hydrogen bonds       : angle       4.60589 ( 1485)
  SS BOND              : bond        0.00817 (    5)
  SS BOND              : angle       2.15838 (   10)
  covalent geometry    : bond        0.00458 (14381)
  covalent geometry    : angle       0.71262 (19538)
  Misc. bond           : bond        0.00184 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
REVERT: A  522 ASN cc_start: 0.9068 (t0) cc_final: 0.8825 (p0)
REVERT: A 1275 MET cc_start: 0.6763 (ptp) cc_final: 0.6222 (ptp)
REVERT: A 1382 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8030 (mt)
  outliers start: 10
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2846
  time to fit residues: 47.4439
Evaluate side-chains
  105 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 HIS
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  744 TYR
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1336 TRP
Chi-restraints excluded: chain A residue 1382 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 179 optimal weight:    8.9990
   chunk 166 optimal weight:   50.0000
   chunk 175 optimal weight:    8.9990
   chunk 127 optimal weight:    1.9990
   chunk 174 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9980
   chunk 101 optimal weight:    0.8980
   chunk 167 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 68 optimal weight:   10.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
A 766 ASN
** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.235070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.193262 restraints weight = 29064.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.4181 rms_B_bonded: 3.41
r_work: 0.3714 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  14387  Z= 0.188
  Angle     :  0.716  11.323  19548  Z= 0.344
  Chirality :  0.044   0.252   2215
  Planarity :  0.005   0.062   2497
  Dihedral  :  9.313 161.317   2055
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.62 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.80 %
    Favored  : 86.04 %
  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: -2.39 (0.20), residues: 1783
  helix: -0.89 (0.17), residues: 890
  sheet: -1.86 (0.44), residues: 149
  loop : -2.32 (0.22), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 500 
 HIS   0.023   0.001   HIS A 181 
 PHE   0.022   0.001   PHE A1486 
 TYR   0.031   0.002   TYR A 744 
 ARG   0.004   0.000   ARG A1705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03723 (  511)
  hydrogen bonds       : angle       4.56454 ( 1485)
  SS BOND              : bond        0.00821 (    5)
  SS BOND              : angle       2.17441 (   10)
  covalent geometry    : bond        0.00460 (14381)
  covalent geometry    : angle       0.71432 (19538)
  Misc. bond           : bond        0.00165 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  441 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8086 (tt)
REVERT: A  522 ASN cc_start: 0.9037 (t0) cc_final: 0.8822 (p0)
REVERT: A 1275 MET cc_start: 0.6791 (ptp) cc_final: 0.6152 (ptp)
REVERT: A 1382 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7998 (mt)
  outliers start: 17
  outliers final: 10
  residues processed: 108
  average time/residue: 0.2061
  time to fit residues: 36.5724
Evaluate side-chains
  107 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  744 TYR
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1336 TRP
Chi-restraints excluded: chain A residue 1382 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 135 optimal weight:    0.0170
   chunk 108 optimal weight:    4.9990
   chunk 177 optimal weight:    0.0370
   chunk 175 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 179 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 85 optimal weight:    0.4980
   chunk 152 optimal weight:    0.5980
   chunk 150 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
A 766 ASN
** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** 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 = 0.4600 r_free = 0.4600 target = 0.239062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.199180 restraints weight = 40580.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.4235 rms_B_bonded: 3.61
r_work: 0.3648 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  14387  Z= 0.108
  Angle     :  0.656   9.913  19548  Z= 0.315
  Chirality :  0.042   0.273   2215
  Planarity :  0.005   0.061   2497
  Dihedral  :  8.795 165.771   2055
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 13.96 %
    Favored  : 85.30 %
  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 (0.20), residues: 1783
  helix: -0.64 (0.18), residues: 884
  sheet: -1.56 (0.45), residues: 147
  loop : -2.23 (0.22), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1480 
 HIS   0.005   0.001   HIS A 181 
 PHE   0.018   0.001   PHE A1240 
 TYR   0.015   0.001   TYR A 744 
 ARG   0.005   0.000   ARG A1705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03035 (  511)
  hydrogen bonds       : angle       4.41272 ( 1485)
  SS BOND              : bond        0.00346 (    5)
  SS BOND              : angle       1.25250 (   10)
  covalent geometry    : bond        0.00250 (14381)
  covalent geometry    : angle       0.65550 (19538)
  Misc. bond           : bond        0.00144 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  441 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7520 (tt)
REVERT: A  749 TRP cc_start: 0.7562 (m100) cc_final: 0.6228 (t60)
REVERT: A  766 ASN cc_start: 0.5929 (m-40) cc_final: 0.5710 (m110)
REVERT: A 1275 MET cc_start: 0.5974 (ptp) cc_final: 0.5414 (ptp)
REVERT: A 1869 MET cc_start: 0.2609 (tpt) cc_final: 0.2282 (tpt)
  outliers start: 11
  outliers final: 8
  residues processed: 115
  average time/residue: 0.2582
  time to fit residues: 46.2543
Evaluate side-chains
  107 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  744 TYR
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1336 TRP
Chi-restraints excluded: chain A residue 1508 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 127 optimal weight:    9.9990
   chunk 113 optimal weight:    0.0270
   chunk 161 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0470
   chunk 101 optimal weight:    0.3980
   chunk 153 optimal weight:   10.0000
   chunk 58 optimal weight:    0.6980
   chunk 112 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.242647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.201727 restraints weight = 35239.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.4270 rms_B_bonded: 3.69
r_work: 0.3772 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3761 r_free = 0.3761    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3761 r_free = 0.3761    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  14387  Z= 0.106
  Angle     :  0.647   9.781  19548  Z= 0.306
  Chirality :  0.041   0.249   2215
  Planarity :  0.005   0.058   2497
  Dihedral  :  8.542 165.990   2055
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 14.77 %
    Favored  : 84.55 %
  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: -1.84 (0.20), residues: 1783
  helix: -0.40 (0.18), residues: 877
  sheet: -1.32 (0.46), residues: 148
  loop : -2.15 (0.22), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 979 
 HIS   0.002   0.000   HIS A 181 
 PHE   0.021   0.001   PHE A1240 
 TYR   0.011   0.001   TYR A 744 
 ARG   0.004   0.000   ARG A1007 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02905 (  511)
  hydrogen bonds       : angle       4.25239 ( 1485)
  SS BOND              : bond        0.00391 (    5)
  SS BOND              : angle       1.22705 (   10)
  covalent geometry    : bond        0.00246 (14381)
  covalent geometry    : angle       0.64615 (19538)
  Misc. bond           : bond        0.00140 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 1.521 
Fit side-chains
   revert: symmetry clash
REVERT: A  441 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7337 (tt)
REVERT: A  749 TRP cc_start: 0.7638 (m100) cc_final: 0.6177 (t60)
REVERT: A  891 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7683 (p)
REVERT: A 1275 MET cc_start: 0.6050 (ptp) cc_final: 0.5598 (pmm)
REVERT: A 1869 MET cc_start: 0.2522 (tpt) cc_final: 0.2239 (tpt)
  outliers start: 10
  outliers final: 7
  residues processed: 112
  average time/residue: 0.2879
  time to fit residues: 50.9962
Evaluate side-chains
  111 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 1.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  744 TYR
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1336 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0770
   chunk 12 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 53 optimal weight:    0.2980
   chunk 63 optimal weight:    0.6980
   chunk 168 optimal weight:    6.9990
   chunk 178 optimal weight:   20.0000
   chunk 68 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 522 ASN
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** 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 = 0.4642 r_free = 0.4642 target = 0.243009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.203680 restraints weight = 43416.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.4281 rms_B_bonded: 3.82
r_work: 0.3822 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3820
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3820 r_free = 0.3820    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3820 r_free = 0.3820    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3820
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  14387  Z= 0.110
  Angle     :  0.648  10.013  19548  Z= 0.307
  Chirality :  0.042   0.256   2215
  Planarity :  0.005   0.058   2497
  Dihedral  :  8.473 165.788   2055
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 14.97 %
    Favored  : 84.28 %
  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: -1.72 (0.20), residues: 1783
  helix: -0.31 (0.18), residues: 875
  sheet: -1.18 (0.46), residues: 148
  loop : -2.10 (0.22), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 979 
 HIS   0.002   0.000   HIS A 939 
 PHE   0.021   0.001   PHE A1240 
 TYR   0.011   0.001   TYR A 744 
 ARG   0.004   0.000   ARG A1007 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02888 (  511)
  hydrogen bonds       : angle       4.17395 ( 1485)
  SS BOND              : bond        0.00413 (    5)
  SS BOND              : angle       1.25394 (   10)
  covalent geometry    : bond        0.00259 (14381)
  covalent geometry    : angle       0.64732 (19538)
  Misc. bond           : bond        0.00121 (    1)

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

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

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3566 Ramachandran restraints generated.
    1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 MET cc_start: 0.7589 (tmm) cc_final: 0.7319 (tmm)
REVERT: A  441 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7363 (tt)
REVERT: A  749 TRP cc_start: 0.7573 (m100) cc_final: 0.6356 (t60)
REVERT: A  891 VAL cc_start: 0.7999 (OUTLIER) cc_final: 0.7754 (p)
REVERT: A 1869 MET cc_start: 0.2597 (tpt) cc_final: 0.2369 (tpt)
  outliers start: 11
  outliers final: 8
  residues processed: 109
  average time/residue: 0.3099
  time to fit residues: 52.1334
Evaluate side-chains
  107 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1336 TRP
Chi-restraints excluded: chain A residue 1508 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 167 optimal weight:   20.0000
   chunk 20 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 77 optimal weight:    0.6980
   chunk 168 optimal weight:    0.0570
   chunk 107 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0970
   chunk 147 optimal weight:    2.9990
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
A 522 ASN
** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** 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 = 0.4641 r_free = 0.4641 target = 0.242970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.202798 restraints weight = 40136.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.4274 rms_B_bonded: 3.81
r_work: 0.3781 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3777
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3777 r_free = 0.3777    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3777 r_free = 0.3777    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110  14387  Z= 0.174
  Angle     :  0.867  59.159  19548  Z= 0.464
  Chirality :  0.043   0.547   2215
  Planarity :  0.005   0.060   2497
  Dihedral  :  8.566 165.787   2055
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.76 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 15.38 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -1.71 (0.20), residues: 1783
  helix: -0.30 (0.18), residues: 875
  sheet: -1.17 (0.46), residues: 148
  loop : -2.08 (0.22), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 979 
 HIS   0.002   0.000   HIS A 939 
 PHE   0.020   0.001   PHE A1240 
 TYR   0.017   0.001   TYR A 744 
 ARG   0.004   0.000   ARG A1007 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02887 (  511)
  hydrogen bonds       : angle       4.17414 ( 1485)
  SS BOND              : bond        0.00407 (    5)
  SS BOND              : angle       1.24858 (   10)
  covalent geometry    : bond        0.00337 (14381)
  covalent geometry    : angle       0.86637 (19538)
  Misc. bond           : bond        0.00113 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7635.39 seconds
wall clock time: 135 minutes 1.11 seconds (8101.11 seconds total)