Starting phenix.real_space_refine
on Fri Feb 14 10:31:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ppu_20447/02_2025/6ppu_20447.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ppu_20447/02_2025/6ppu_20447.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ppu_20447/02_2025/6ppu_20447.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ppu_20447/02_2025/6ppu_20447.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ppu_20447/02_2025/6ppu_20447.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ppu_20447/02_2025/6ppu_20447.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      29      5.49       5
     Mg      1      5.21       5
     S      32      5.16       5
     C    6299      2.51       5
     N    1867      2.21       5
     O    1872      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10104
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 5359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 752, 5359
          Classifications: {'peptide': 752}
          Incomplete info: {'truncation_to_alanine': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 705}
          Chain breaks: 17
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 404
          Unresolved non-hydrogen angles: 508
          Unresolved non-hydrogen dihedrals: 320
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 1, 'GLU:plan': 29, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 301
    Chain: "A"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 1932
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 90}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280}
          Chain breaks: 15
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 288
          Unresolved non-hydrogen angles: 378
          Unresolved non-hydrogen dihedrals: 209
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 9, 'TYR:plan': 1, 'UNK:plan-1': 38, 'HIS:plan': 3, 'GLU:plan': 7, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 204
    Chain: "A"
      Number of atoms: 2212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2212
          Classifications: {'peptide': 309}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 22, 'TRANS': 286}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 133
          Unresolved non-hydrogen angles: 169
          Unresolved non-hydrogen dihedrals: 97
          Planarities with less than four sites: {'GLU:plan': 14, 'UNK:plan-1': 13, 'ASP:plan': 5, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 104
    Chain: "X"
      Number of atoms: 592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 592
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 9
          Unusual residues: {' MG': 1, 'SF4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.58, per 1000 atoms: 0.65
  Number of scatterers: 10104
  At special positions: 0
  Unit cell: (123.166, 95.6043, 112.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      4     26.01
     S      32     16.00
     P      29     15.00
     Mg      1     11.99
     O    1872      8.00
     N    1867      7.00
     C    6299      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1102 "
        pdb="FE4  SF4 A1102 " - pdb=" SG  CYS A 807 "
        pdb="FE1  SF4 A1102 " - pdb=" SG  CYS A1030 "
        pdb="FE2  SF4 A1102 " - pdb=" SG  CYS A1036 "
      Number of angles added : 9


  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2534

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 6 sheets defined
      48.4% alpha, 5.8% beta
      4 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 3.19
  Creating SS restraints...
    Processing helix  chain 'B' and resid 31 through 36
    Processing helix  chain 'B' and resid 52 through 55
    Processing helix  chain 'B' and resid 56 through 63
      removed outlier: 3.617A  pdb=" N   VAL B  60 " --> pdb=" O   MET B  56 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   TRP B  62 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 98
      removed outlier: 3.710A  pdb=" N   GLY B  85 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LEU B  87 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL B  91 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG B  92 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   ARG B  94 " --> pdb=" O   ARG B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 130
      removed outlier: 4.124A  pdb=" N   GLY B 124 " --> pdb=" O   HIS B 120 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   HIS B 130 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 157
      removed outlier: 3.751A  pdb=" N   LEU B 151 " --> pdb=" O   GLU B 147 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP B 154 " --> pdb=" O   GLN B 150 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 180
    Processing helix  chain 'B' and resid 200 through 206
      removed outlier: 3.736A  pdb=" N   VAL B 204 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   HIS B 205 " --> pdb=" O   GLU B 201 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   THR B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 200 through 206'
    Processing helix  chain 'B' and resid 220 through 228
      removed outlier: 3.941A  pdb=" N   ARG B 224 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   MET B 225 " --> pdb=" O   TRP B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 233
      removed outlier: 3.732A  pdb=" N   ARG B 232 " --> pdb=" O   THR B 228 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   THR B 233 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 228 through 233'
    Processing helix  chain 'B' and resid 235 through 239
    Processing helix  chain 'B' and resid 242 through 247
    Processing helix  chain 'B' and resid 253 through 262
      removed outlier: 3.953A  pdb=" N   MET B 258 " --> pdb=" O   PHE B 254 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA B 259 " --> pdb=" O   GLY B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 279
      removed outlier: 4.023A  pdb=" N   GLY B 272 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU B 275 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 290
      removed outlier: 3.930A  pdb=" N   ASP B 289 " --> pdb=" O   GLU B 286 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   THR B 290 " --> pdb=" O   TYR B 287 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 286 through 290'
    Processing helix  chain 'B' and resid 297 through 302
      removed outlier: 3.736A  pdb=" N   LEU B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 372
    Processing helix  chain 'B' and resid 402 through 416
      removed outlier: 3.690A  pdb=" N   ALA B 411 " --> pdb=" O   ARG B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 452
      removed outlier: 3.874A  pdb=" N   MET B 444 " --> pdb=" O   ASP B 440 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLY B 452 " --> pdb=" O   LEU B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 466
      removed outlier: 3.830A  pdb=" N   ALA B 465 " --> pdb=" O   GLY B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 481
      removed outlier: 3.811A  pdb=" N   LEU B 472 " --> pdb=" O   GLU B 468 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LEU B 476 " --> pdb=" O   LEU B 472 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ILE B 479 " --> pdb=" O   MET B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 488
      removed outlier: 3.620A  pdb=" N   ALA B 487 " --> pdb=" O   ALA B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 514
      removed outlier: 3.616A  pdb=" N   ALA B 505 " --> pdb=" O   ALA B 501 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG B 509 " --> pdb=" O   ALA B 505 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG B 510 " --> pdb=" O   ALA B 506 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU B 513 " --> pdb=" O   ARG B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 530
      removed outlier: 4.029A  pdb=" N   GLN B 530 " --> pdb=" O   ASP B 526 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 543
      removed outlier: 4.048A  pdb=" N   ASP B 542 " --> pdb=" O   CYS B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 573
      removed outlier: 3.722A  pdb=" N   ILE B 561 " --> pdb=" O   GLY B 557 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR B 569 " --> pdb=" O   GLY B 565 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   MET B 570 " --> pdb=" O   ARG B 566 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ALA B 573 " --> pdb=" O   THR B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 590
      removed outlier: 3.773A  pdb=" N   ARG B 588 " --> pdb=" O   ALA B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 605
      removed outlier: 3.575A  pdb=" N   ALA B 604 " --> pdb=" O   PRO B 601 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLY B 605 " --> pdb=" O   VAL B 602 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 601 through 605'
    Processing helix  chain 'B' and resid 610 through 623
      removed outlier: 3.668A  pdb=" N   PHE B 615 " --> pdb=" O   ASN B 611 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER B 616 " --> pdb=" O   LEU B 612 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASP B 617 " --> pdb=" O   ASP B 613 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   SER B 620 " --> pdb=" O   SER B 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 643
      removed outlier: 3.765A  pdb=" N   GLU B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 735 through 748
      removed outlier: 3.519A  pdb=" N   LYS B 740 " --> pdb=" O   SER B 736 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ARG B 745 " --> pdb=" O   SER B 741 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ARG B 746 " --> pdb=" O   LEU B 742 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL B 747 " --> pdb=" O   ASP B 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 759
      removed outlier: 3.944A  pdb=" N   THR B 759 " --> pdb=" O   TYR B 755 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 783 through 794
      removed outlier: 3.649A  pdb=" N   THR B 791 " --> pdb=" O   CYS B 787 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU B 794 " --> pdb=" O   LYS B 790 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 839 through 851
      removed outlier: 3.612A  pdb=" N   GLN B 845 " --> pdb=" O   HIS B 841 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU B 846 " --> pdb=" O   ARG B 842 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL B 847 " --> pdb=" O   GLY B 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 863 through 876
      removed outlier: 3.546A  pdb=" N   ASP B 867 " --> pdb=" O   GLY B 863 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   VAL B 868 " --> pdb=" O   TRP B 864 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP B 869 " --> pdb=" O   ALA B 865 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA B 873 " --> pdb=" O   ASP B 869 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLU B 874 " --> pdb=" O   ALA B 870 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG B 875 " --> pdb=" O   LEU B 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 179
      No H-bonds generated for 'chain 'A' and resid 177 through 179'
    Processing helix  chain 'A' and resid 180 through 185
      removed outlier: 3.531A  pdb=" N   UNK A 185 " --> pdb=" O   UNK A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 196
      removed outlier: 4.147A  pdb=" N   UNK A 191 " --> pdb=" O   UNK A 187 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   UNK A 193 " --> pdb=" O   UNK A 189 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   UNK A 194 " --> pdb=" O   UNK A 190 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   UNK A 196 " --> pdb=" O   UNK A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 321
    Processing helix  chain 'A' and resid 356 through 374
      removed outlier: 3.892A  pdb=" N   ILE A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 373 " --> pdb=" O   ARG A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 404
      removed outlier: 3.530A  pdb=" N   ALA A 403 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 433
      removed outlier: 3.598A  pdb=" N   ALA A 423 " --> pdb=" O   GLN A 419 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU A 425 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   VAL A 428 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A 429 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR A 432 " --> pdb=" O   VAL A 428 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 447
      removed outlier: 3.965A  pdb=" N   ALA A 442 " --> pdb=" O   ASP A 438 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A 443 " --> pdb=" O   ALA A 439 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ALA A 444 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 469
      removed outlier: 3.684A  pdb=" N   ARG A 463 " --> pdb=" O   ARG A 459 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA A 464 " --> pdb=" O   GLN A 460 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   ARG A 467 " --> pdb=" O   ARG A 463 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA A 468 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 487
      removed outlier: 3.656A  pdb=" N   VAL A 482 " --> pdb=" O   GLY A 478 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASP A 483 " --> pdb=" O   ASP A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 508
      removed outlier: 3.682A  pdb=" N   THR A 499 " --> pdb=" O   GLU A 495 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU A 500 " --> pdb=" O   HIS A 496 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 503 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL A 506 " --> pdb=" O   ARG A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 531
      removed outlier: 3.508A  pdb=" N   TRP A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A 530 " --> pdb=" O   GLN A 526 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER A 531 " --> pdb=" O   ALA A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 540
    Processing helix  chain 'A' and resid 547 through 569
      removed outlier: 3.639A  pdb=" N   ALA A 551 " --> pdb=" O   VAL A 547 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG A 553 " --> pdb=" O   ALA A 549 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ALA A 557 " --> pdb=" O   ARG A 553 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   THR A 559 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   THR A 560 " --> pdb=" O   ASP A 556 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 561 " --> pdb=" O   ALA A 557 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE A 562 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   VAL A 564 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 586
      removed outlier: 4.165A  pdb=" N   ASP A 582 " --> pdb=" O   ARG A 578 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A 584 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   THR A 585 " --> pdb=" O   VAL A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 647
    Processing helix  chain 'A' and resid 701 through 707
      removed outlier: 3.714A  pdb=" N   UNK A 707 " --> pdb=" O   UNK A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 740
      removed outlier: 3.512A  pdb=" N   VAL A 732 " --> pdb=" O   PRO A 728 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLY A 733 " --> pdb=" O   SER A 729 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG A 736 " --> pdb=" O   VAL A 732 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA A 737 " --> pdb=" O   GLY A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 763
      removed outlier: 3.609A  pdb=" N   GLN A 757 " --> pdb=" O   CYS A 753 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A 760 " --> pdb=" O   ALA A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 803
      removed outlier: 3.671A  pdb=" N   GLN A 802 " --> pdb=" O   PRO A 798 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   MET A 803 " --> pdb=" O   SER A 799 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 798 through 803'
    Processing helix  chain 'A' and resid 809 through 815
      removed outlier: 3.524A  pdb=" N   ARG A 815 " --> pdb=" O   TRP A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 827
    Processing helix  chain 'A' and resid 828 through 838
      removed outlier: 3.696A  pdb=" N   HIS A 833 " --> pdb=" O   GLY A 829 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA A 834 " --> pdb=" O   SER A 830 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A 835 " --> pdb=" O   LEU A 831 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   SER A 837 " --> pdb=" O   HIS A 833 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   GLU A 838 " --> pdb=" O   ALA A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 854
      removed outlier: 3.614A  pdb=" N   VAL A 847 " --> pdb=" O   GLU A 843 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LYS A 852 " --> pdb=" O   ASN A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 873
      removed outlier: 4.570A  pdb=" N   LEU A 869 " --> pdb=" O   SER A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 874 through 884
      removed outlier: 4.145A  pdb=" N   THR A 880 " --> pdb=" O   LEU A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 961
      removed outlier: 3.856A  pdb=" N   TYR A 956 " --> pdb=" O   GLN A 952 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LEU A 958 " --> pdb=" O   ALA A 954 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA A 961 " --> pdb=" O   GLN A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1001
      removed outlier: 3.899A  pdb=" N   ALA A1001 " --> pdb=" O   PRO A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1012
      removed outlier: 3.836A  pdb=" N   VAL A1007 " --> pdb=" O   TRP A1003 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY A1008 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA A1012 " --> pdb=" O   GLY A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1015
      No H-bonds generated for 'chain 'A' and resid 1013 through 1015'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 116 through 118
      removed outlier: 7.614A  pdb=" N   SER B 117 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   GLY B  76 " --> pdb=" O   SER B 117 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   LEU B  75 " --> pdb=" O   LEU B 283 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142
      removed outlier: 6.635A  pdb=" N   ARG B 141 " --> pdb=" O   MET B 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 395 through 397
      removed outlier: 6.004A  pdb=" N   ARG B 396 " --> pdb=" O   LEU B 767 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   VAL B 675 " --> pdb=" O   LEU B 766 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA B 676 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 829 through 830
    Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 354
      removed outlier: 6.744A  pdb=" N   THR A 350 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 8.508A  pdb=" N   ALA A 688 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ARG A 352 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   VAL A 619 " --> pdb=" O   MET A 685 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   THR A 687 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ILE A 621 " --> pdb=" O   THR A 687 " (cutoff:3.500A)
      removed outlier: 8.722A  pdb=" N   VAL A 689 " --> pdb=" O   ILE A 621 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ALA A 383 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   ALA A 622 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ILE A 385 " --> pdb=" O   ALA A 622 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL A 384 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 891 through 897
      removed outlier: 7.308A  pdb=" N   LEU A 922 " --> pdb=" O   VAL A 893 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   THR A 895 " --> pdb=" O   ASP A 920 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ASP A 920 " --> pdb=" O   THR A 895 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG A 921 " --> pdb=" O   VAL A 933 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LEU A 930 " --> pdb=" O   GLY A 973 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   LYS A 975 " --> pdb=" O   LEU A 930 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   VAL A 932 " --> pdb=" O   LYS A 975 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   VAL A 977 " --> pdb=" O   VAL A 932 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLN A 992 " --> pdb=" O   GLY A 974 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR A 978 " --> pdb=" O   THR A 988 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   THR A 988 " --> pdb=" O   TYR A 978 " (cutoff:3.500A)

    269 hydrogen bonds defined for protein.
    771 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      8 hydrogen bonds
      16 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 3.23

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.43: 4180
        1.43 -     1.64: 6087
        1.64 -     1.85: 45
        1.85 -     2.06: 0
        2.06 -     2.28: 12
  Bond restraints: 10324
  Sorted by residual:
  bond pdb=" N   THR A 795 "
       pdb=" CA  THR A 795 "
    ideal  model  delta    sigma   weight residual
    1.457  1.508 -0.051 1.29e-02 6.01e+03 1.56e+01
  bond pdb=" N   VAL A 794 "
       pdb=" CA  VAL A 794 "
    ideal  model  delta    sigma   weight residual
    1.460  1.506 -0.046 1.19e-02 7.06e+03 1.48e+01
  bond pdb=" N   VAL A 793 "
       pdb=" CA  VAL A 793 "
    ideal  model  delta    sigma   weight residual
    1.459  1.504 -0.044 1.29e-02 6.01e+03 1.19e+01
  bond pdb=" N   VAL A 904 "
       pdb=" CA  VAL A 904 "
    ideal  model  delta    sigma   weight residual
    1.458  1.497 -0.039 1.17e-02 7.31e+03 1.10e+01
  bond pdb=" N   VAL A 915 "
       pdb=" CA  VAL A 915 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.19e-02 7.06e+03 1.00e+01
  ... (remaining 10319 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 13174
        2.05 -     4.10: 897
        4.10 -     6.15: 113
        6.15 -     8.21: 37
        8.21 -    10.26: 17
  Bond angle restraints: 14238
  Sorted by residual:
  angle pdb=" N   VAL B 488 "
        pdb=" CA  VAL B 488 "
        pdb=" C   VAL B 488 "
      ideal   model   delta    sigma   weight residual
     111.90  105.31    6.59 8.10e-01 1.52e+00 6.62e+01
  angle pdb=" N   VAL A 794 "
        pdb=" CA  VAL A 794 "
        pdb=" C   VAL A 794 "
      ideal   model   delta    sigma   weight residual
     110.53  117.95   -7.42 9.40e-01 1.13e+00 6.23e+01
  angle pdb=" N   LEU B 476 "
        pdb=" CA  LEU B 476 "
        pdb=" C   LEU B 476 "
      ideal   model   delta    sigma   weight residual
     113.12  104.52    8.60 1.25e+00 6.40e-01 4.73e+01
  angle pdb=" N   THR B 338 "
        pdb=" CA  THR B 338 "
        pdb=" C   THR B 338 "
      ideal   model   delta    sigma   weight residual
     114.56  106.74    7.82 1.27e+00 6.20e-01 3.79e+01
  angle pdb=" C   THR B 449 "
        pdb=" N   ALA B 450 "
        pdb=" CA  ALA B 450 "
      ideal   model   delta    sigma   weight residual
     120.28  127.80   -7.52 1.34e+00 5.57e-01 3.15e+01
  ... (remaining 14233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.58: 5884
       35.58 -    71.16: 148
       71.16 -   106.73: 5
      106.73 -   142.31: 3
      142.31 -   177.89: 2
  Dihedral angle restraints: 6042
    sinusoidal: 2182
      harmonic: 3860
  Sorted by residual:
  dihedral pdb=" CA  ASP B 189 "
           pdb=" C   ASP B 189 "
           pdb=" N   THR B 190 "
           pdb=" CA  THR B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.13   28.87     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  SER B 362 "
           pdb=" C   SER B 362 "
           pdb=" N   THR B 363 "
           pdb=" CA  THR B 363 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.26   27.74     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" CA  TYR A 859 "
           pdb=" C   TYR A 859 "
           pdb=" N   ASP A 860 "
           pdb=" CA  ASP A 860 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.24   25.76     0      5.00e+00 4.00e-02 2.66e+01
  ... (remaining 6039 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1366
       0.071 -    0.143: 324
       0.143 -    0.214: 65
       0.214 -    0.286: 6
       0.286 -    0.357: 2
  Chirality restraints: 1763
  Sorted by residual:
  chirality pdb=" CA  THR A 795 "
            pdb=" N   THR A 795 "
            pdb=" C   THR A 795 "
            pdb=" CB  THR A 795 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" C3'  DT X   2 "
            pdb=" C4'  DT X   2 "
            pdb=" O3'  DT X   2 "
            pdb=" C2'  DT X   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.32   -0.35 2.00e-01 2.50e+01 2.98e+00
  chirality pdb=" CA  ARG A 914 "
            pdb=" N   ARG A 914 "
            pdb=" C   ARG A 914 "
            pdb=" CB  ARG A 914 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 1760 not shown)

  Planarity restraints: 1715
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 532 "   -0.057 5.00e-02 4.00e+02   8.59e-02 1.18e+01
        pdb=" N   PRO B 533 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO B 533 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B 533 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 217 "    0.047 5.00e-02 4.00e+02   7.08e-02 8.02e+00
        pdb=" N   PRO B 218 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO B 218 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 218 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 435 "   -0.014 2.00e-02 2.50e+03   2.81e-02 7.90e+00
        pdb=" C   VAL B 435 "    0.049 2.00e-02 2.50e+03
        pdb=" O   VAL B 435 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ARG B 436 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1712 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 21
        2.46 -     3.07: 5729
        3.07 -     3.68: 14376
        3.68 -     4.29: 19869
        4.29 -     4.90: 33108
  Nonbonded interactions: 73103
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 336 "
            pdb=" OG1 THR B 337 "
     model   vdw
     1.855 3.040
  nonbonded pdb=" O   LEU B 522 "
            pdb=" OD2 ASP B 526 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" CG2 THR A 447 "
            pdb=" CG2 VAL A 453 "
     model   vdw
     2.269 3.880
  nonbonded pdb=" CD2 HIS B 130 "
            pdb=" CG1 VAL B 271 "
     model   vdw
     2.310 3.680
  nonbonded pdb=" OD2 ASP B 867 "
            pdb=" NH2 ARG A 724 "
     model   vdw
     2.341 3.120
  ... (remaining 73098 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  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:             0.000
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     29.790
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.078  10324  Z= 0.565
  Angle     :  1.177  10.257  14238  Z= 0.695
  Chirality :  0.065   0.357   1763
  Planarity :  0.008   0.086   1715
  Dihedral  : 15.183 177.887   3508
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  :  6.44 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -5.80 (0.18), residues: 1226
  helix: -4.40 (0.12), residues: 621
  sheet: -2.73 (0.55), residues: 96
  loop : -3.11 (0.24), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.004   TRP B 497 
 HIS   0.010   0.002   HIS B 577 
 PHE   0.016   0.003   PHE B 685 
 TYR   0.027   0.003   TYR A 956 
 ARG   0.015   0.001   ARG B 572 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 195
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
REVERT: A  819 ASP cc_start: 0.8103 (t0) cc_final: 0.7776 (t0)
REVERT: A  913 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7578 (t)
REVERT: A 1025 ASN cc_start: 0.7729 (t0) cc_final: 0.7356 (t0)
  outliers start: 26
  outliers final: 10
  residues processed: 212
  average time/residue: 0.2645
  time to fit residues: 74.6692
Evaluate side-chains
  125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  671 GLU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  441 SER
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  914 ARG
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  919 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0040
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0980
   chunk 79 optimal weight:    2.9990
   chunk 123 optimal weight:    0.7980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
B  66 ASN
B 130 HIS
B 294 GLN
B 413 HIS
B 738 HIS
B 770 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.160698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.135865 restraints weight = 14172.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.133892 restraints weight = 12456.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.135081 restraints weight = 11512.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10324  Z= 0.178
  Angle     :  0.651  11.138  14238  Z= 0.337
  Chirality :  0.041   0.239   1763
  Planarity :  0.005   0.052   1715
  Dihedral  : 16.664 175.242   1745
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.20 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 13.23 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -4.61 (0.20), residues: 1226
  helix: -3.38 (0.15), residues: 622
  sheet: -2.72 (0.54), residues: 92
  loop : -2.48 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 497 
 HIS   0.009   0.001   HIS A 372 
 PHE   0.037   0.002   PHE B  68 
 TYR   0.012   0.001   TYR A 859 
 ARG   0.006   0.001   ARG B 683 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 1.035 
Fit side-chains
REVERT: A 1025 ASN cc_start: 0.7410 (t0) cc_final: 0.7109 (t0)
  outliers start: 25
  outliers final: 12
  residues processed: 160
  average time/residue: 0.2550
  time to fit residues: 55.5880
Evaluate side-chains
  106 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  613 ASP
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  671 GLU
Chi-restraints excluded: chain B residue  786 LEU
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain A residue  914 ARG
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1014 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 125 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 116 optimal weight:    5.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 243 HIS
** A 372 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 = 0.3753 r_free = 0.3753 target = 0.158006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.133614 restraints weight = 14143.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.131767 restraints weight = 13140.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.132006 restraints weight = 11223.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10324  Z= 0.215
  Angle     :  0.625   7.801  14238  Z= 0.322
  Chirality :  0.041   0.153   1763
  Planarity :  0.005   0.056   1715
  Dihedral  : 16.510 173.070   1734
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.44 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 13.71 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -3.79 (0.22), residues: 1226
  helix: -2.53 (0.18), residues: 627
  sheet: -2.12 (0.54), residues: 104
  loop : -2.35 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 497 
 HIS   0.008   0.001   HIS A 372 
 PHE   0.016   0.001   PHE B  68 
 TYR   0.012   0.001   TYR A 956 
 ARG   0.004   0.000   ARG B 178 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 0.979 
Fit side-chains
REVERT: B  829 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8377 (mp)
REVERT: A  577 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6902 (pp)
  outliers start: 31
  outliers final: 20
  residues processed: 127
  average time/residue: 0.2104
  time to fit residues: 38.9600
Evaluate side-chains
  119 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  613 ASP
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  786 LEU
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  738 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1014 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 111 optimal weight:    0.0370
   chunk 104 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 135 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 96 optimal weight:   10.0000
   chunk 121 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   overall best weight:    2.4066

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

Flipped N/Q/H residues before XYZ refinement:
B  66 ASN
B 679 HIS
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.153541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.128020 restraints weight = 14100.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.126714 restraints weight = 13625.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.127565 restraints weight = 13481.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  10324  Z= 0.400
  Angle     :  0.714   9.658  14238  Z= 0.364
  Chirality :  0.046   0.176   1763
  Planarity :  0.005   0.053   1715
  Dihedral  : 16.742 168.145   1726
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 13.11 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -3.50 (0.22), residues: 1226
  helix: -2.33 (0.18), residues: 622
  sheet: -1.48 (0.58), residues: 96
  loop : -2.31 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 497 
 HIS   0.010   0.002   HIS A 775 
 PHE   0.016   0.002   PHE B 340 
 TYR   0.017   0.002   TYR A 864 
 ARG   0.004   0.001   ARG A1000 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 96
  time to evaluate  : 1.082 
Fit side-chains
REVERT: B   66 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8072 (t0)
REVERT: B   68 PHE cc_start: 0.8436 (m-80) cc_final: 0.8128 (m-80)
REVERT: B  497 TRP cc_start: 0.8782 (OUTLIER) cc_final: 0.8125 (p90)
REVERT: B  754 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8799 (tp)
REVERT: A  577 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6830 (pp)
REVERT: A  777 MET cc_start: 0.8312 (mmm) cc_final: 0.8089 (mmm)
  outliers start: 54
  outliers final: 33
  residues processed: 139
  average time/residue: 0.2001
  time to fit residues: 41.2114
Evaluate side-chains
  131 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 94
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 ASN
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  252 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  497 TRP
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  539 CYS
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  613 ASP
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  786 LEU
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  738 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  820 ASP
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  996 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 31 optimal weight:    0.0770
   chunk 74 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0020
   chunk 75 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.9148

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.156397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.129357 restraints weight = 14126.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.128824 restraints weight = 16171.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.130201 restraints weight = 13701.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10324  Z= 0.191
  Angle     :  0.594   7.326  14238  Z= 0.303
  Chirality :  0.040   0.151   1763
  Planarity :  0.004   0.052   1715
  Dihedral  : 16.528 171.575   1726
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.33 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -2.92 (0.23), residues: 1226
  helix: -1.77 (0.20), residues: 613
  sheet: -1.67 (0.56), residues: 101
  loop : -2.04 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 497 
 HIS   0.004   0.001   HIS A 372 
 PHE   0.010   0.001   PHE B 340 
 TYR   0.011   0.001   TYR A 859 
 ARG   0.004   0.000   ARG B  97 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 1.056 
Fit side-chains
REVERT: B   66 ASN cc_start: 0.8189 (t0) cc_final: 0.7928 (t0)
REVERT: B   68 PHE cc_start: 0.8222 (m-80) cc_final: 0.8012 (m-80)
REVERT: B  497 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.8017 (p90)
REVERT: B  754 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8776 (tp)
REVERT: B  829 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8409 (mp)
REVERT: A  577 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6798 (pp)
REVERT: A  777 MET cc_start: 0.8214 (mmm) cc_final: 0.7933 (mmm)
REVERT: A  789 GLU cc_start: 0.7533 (pm20) cc_final: 0.6895 (tp30)
REVERT: A  812 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8877 (tp)
  outliers start: 30
  outliers final: 21
  residues processed: 121
  average time/residue: 0.1885
  time to fit residues: 34.0811
Evaluate side-chains
  108 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  497 TRP
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  613 ASP
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  786 LEU
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  738 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1003 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0970
   chunk 64 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 68 optimal weight:    9.9990
   chunk 14 optimal weight:    0.7980
   chunk 119 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 104 optimal weight:   10.0000
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 162 HIS
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.152976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.127044 restraints weight = 14189.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.126257 restraints weight = 14729.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.127276 restraints weight = 14903.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10324  Z= 0.393
  Angle     :  0.691   8.920  14238  Z= 0.352
  Chirality :  0.045   0.173   1763
  Planarity :  0.005   0.053   1715
  Dihedral  : 16.694 169.606   1726
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 15.73 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -2.99 (0.23), residues: 1226
  helix: -1.77 (0.20), residues: 623
  sheet: -1.57 (0.56), residues: 101
  loop : -2.19 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 379 
 HIS   0.009   0.002   HIS A 775 
 PHE   0.017   0.002   PHE B 340 
 TYR   0.016   0.002   TYR A 859 
 ARG   0.005   0.001   ARG B  97 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 92
  time to evaluate  : 1.019 
Fit side-chains
REVERT: B  497 TRP cc_start: 0.8843 (OUTLIER) cc_final: 0.8242 (p90)
REVERT: A  577 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6773 (pp)
REVERT: A  777 MET cc_start: 0.8305 (mmm) cc_final: 0.8044 (mmm)
REVERT: A  789 GLU cc_start: 0.7562 (pm20) cc_final: 0.7038 (tp30)
  outliers start: 45
  outliers final: 31
  residues processed: 127
  average time/residue: 0.2092
  time to fit residues: 38.7764
Evaluate side-chains
  123 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 90
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  252 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  497 TRP
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  613 ASP
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  786 LEU
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  738 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  820 ASP
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1003 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 118 optimal weight:    0.5980
   chunk 112 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN
** A 372 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 = 0.3733 r_free = 0.3733 target = 0.156409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.129868 restraints weight = 14280.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.129315 restraints weight = 15173.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.131015 restraints weight = 13986.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10324  Z= 0.172
  Angle     :  0.576   7.548  14238  Z= 0.294
  Chirality :  0.040   0.143   1763
  Planarity :  0.004   0.052   1715
  Dihedral  : 16.375 177.005   1726
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.28 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -2.43 (0.23), residues: 1226
  helix: -1.28 (0.20), residues: 626
  sheet: -1.40 (0.56), residues: 101
  loop : -1.94 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 379 
 HIS   0.004   0.001   HIS B 130 
 PHE   0.023   0.001   PHE B  68 
 TYR   0.009   0.001   TYR A 859 
 ARG   0.005   0.000   ARG B  97 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 1.024 
Fit side-chains
REVERT: B  497 TRP cc_start: 0.8784 (OUTLIER) cc_final: 0.8122 (p90)
REVERT: A  577 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6751 (pp)
REVERT: A  777 MET cc_start: 0.8228 (mmm) cc_final: 0.7963 (mmm)
REVERT: A  789 GLU cc_start: 0.7366 (pm20) cc_final: 0.6976 (tp30)
REVERT: A  812 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8880 (tp)
  outliers start: 27
  outliers final: 21
  residues processed: 117
  average time/residue: 0.2173
  time to fit residues: 36.8343
Evaluate side-chains
  114 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  497 TRP
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  613 ASP
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  786 LEU
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1003 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 106 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 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 = 0.3711 r_free = 0.3711 target = 0.155073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.129018 restraints weight = 14266.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.128085 restraints weight = 15701.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.129161 restraints weight = 15062.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10324  Z= 0.267
  Angle     :  0.617   7.909  14238  Z= 0.315
  Chirality :  0.042   0.154   1763
  Planarity :  0.005   0.051   1715
  Dihedral  : 16.390 176.485   1726
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.52 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -2.32 (0.23), residues: 1226
  helix: -1.13 (0.21), residues: 625
  sheet: -1.35 (0.56), residues: 101
  loop : -1.99 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 379 
 HIS   0.006   0.001   HIS A 775 
 PHE   0.021   0.002   PHE B  68 
 TYR   0.013   0.001   TYR A 859 
 ARG   0.006   0.000   ARG B  97 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 89
  time to evaluate  : 1.057 
Fit side-chains
REVERT: B  497 TRP cc_start: 0.8814 (OUTLIER) cc_final: 0.8199 (p90)
REVERT: A  577 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6770 (pp)
REVERT: A  777 MET cc_start: 0.8266 (mmm) cc_final: 0.8017 (mmm)
REVERT: A  789 GLU cc_start: 0.7386 (pm20) cc_final: 0.6969 (tp30)
  outliers start: 31
  outliers final: 28
  residues processed: 111
  average time/residue: 0.2051
  time to fit residues: 33.8131
Evaluate side-chains
  118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  252 MET
Chi-restraints excluded: chain B residue  497 TRP
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  613 ASP
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  786 LEU
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  738 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  820 ASP
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  920 ASP
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1003 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0870
   chunk 116 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 56 optimal weight:    0.0470
   chunk 59 optimal weight:    0.1980
   chunk 73 optimal weight:    7.9990
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 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 = 0.3770 r_free = 0.3770 target = 0.160313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.134353 restraints weight = 14144.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.133417 restraints weight = 16575.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.135579 restraints weight = 14106.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10324  Z= 0.140
  Angle     :  0.543   7.772  14238  Z= 0.279
  Chirality :  0.039   0.142   1763
  Planarity :  0.004   0.051   1715
  Dihedral  : 16.061 178.012   1726
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.07 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -1.85 (0.24), residues: 1226
  helix: -0.71 (0.21), residues: 643
  sheet: -1.19 (0.55), residues: 99
  loop : -1.81 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 379 
 HIS   0.005   0.001   HIS B 130 
 PHE   0.020   0.001   PHE B  68 
 TYR   0.006   0.001   TYR A 859 
 ARG   0.006   0.000   ARG B  97 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 1.009 
Fit side-chains
REVERT: B  117 SER cc_start: 0.8840 (p) cc_final: 0.8635 (m)
REVERT: A  577 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6777 (pp)
  outliers start: 22
  outliers final: 16
  residues processed: 123
  average time/residue: 0.2078
  time to fit residues: 37.1104
Evaluate side-chains
  111 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  786 LEU
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1003 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0570
   chunk 124 optimal weight:    1.9990
   chunk 89 optimal weight:    0.4980
   chunk 61 optimal weight:    0.7980
   chunk 73 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9990
   chunk 100 optimal weight:    0.1980
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 372 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.159942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.135279 restraints weight = 14117.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.133391 restraints weight = 13677.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.134674 restraints weight = 11865.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10324  Z= 0.148
  Angle     :  0.541   7.991  14238  Z= 0.276
  Chirality :  0.039   0.143   1763
  Planarity :  0.004   0.054   1715
  Dihedral  : 15.960 177.882   1726
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 20.02 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -1.53 (0.25), residues: 1226
  helix: -0.43 (0.22), residues: 643
  sheet: -0.89 (0.57), residues: 96
  loop : -1.74 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 379 
 HIS   0.008   0.001   HIS B 130 
 PHE   0.020   0.001   PHE B  68 
 TYR   0.009   0.001   TYR A 859 
 ARG   0.007   0.000   ARG B  97 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 1.182 
Fit side-chains
REVERT: A  577 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6902 (pp)
  outliers start: 18
  outliers final: 16
  residues processed: 102
  average time/residue: 0.2120
  time to fit residues: 32.2869
Evaluate side-chains
  103 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  786 LEU
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  738 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1003 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 127 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 123 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.157261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.131761 restraints weight = 14114.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.132154 restraints weight = 13482.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.132113 restraints weight = 12634.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10324  Z= 0.215
  Angle     :  0.584   7.595  14238  Z= 0.297
  Chirality :  0.041   0.142   1763
  Planarity :  0.004   0.052   1715
  Dihedral  : 16.087 179.337   1726
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.14 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.74 %
    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: -1.54 (0.24), residues: 1226
  helix: -0.44 (0.21), residues: 645
  sheet: -0.94 (0.56), residues: 99
  loop : -1.74 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 497 
 HIS   0.008   0.001   HIS B 130 
 PHE   0.020   0.001   PHE B  68 
 TYR   0.013   0.001   TYR A 859 
 ARG   0.006   0.000   ARG B  97 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2938.45 seconds
wall clock time: 53 minutes 13.64 seconds (3193.64 seconds total)