Starting phenix.real_space_refine
on Tue Apr  7 19:31:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rag_53877/04_2026/9rag_53877.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rag_53877/04_2026/9rag_53877.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rag_53877/04_2026/9rag_53877.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rag_53877/04_2026/9rag_53877.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rag_53877/04_2026/9rag_53877.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rag_53877/04_2026/9rag_53877.cif"
  }
  resolution = 1.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.094
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
     P      49      5.49       5
     Mg      3      5.21       5
     S     103      5.16       5
     C    9186      2.51       5
     N    2590      2.21       5
     O    3600      1.98       5
     H   14344      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 29875
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 11590
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 716, 11546
          Classifications: {'peptide': 716}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 682}
      Conformer: "B"
        Number of residues, atoms: 716, 11546
          Classifications: {'peptide': 716}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 682}
          bond proxies already assigned to first conformer: 11624
    Chain: "C"
      Number of atoms: 4140
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 4084
          Classifications: {'peptide': 248}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 235}
      Conformer: "B"
        Number of residues, atoms: 248, 4084
          Classifications: {'peptide': 248}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 235}
          bond proxies already assigned to first conformer: 4065
    Chain: "G"
      Number of atoms: 351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 351
          Classifications: {'peptide': 25}
          Link IDs: {'PTRANS': 7, 'TRANS': 17}
    Chain: "M"
      Number of atoms: 361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 361
          Classifications: {'RNA': 11}
          Modifications used: {'3*END': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4}
          Link IDs: {'rna3p': 10}
    Chain: "B"
      Number of atoms: 11688
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 726, 11598
          Classifications: {'peptide': 726}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 695}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 726, 11598
          Classifications: {'peptide': 726}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 695}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 11615
    Chain: "T"
      Number of atoms: 1066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 1066
          Classifications: {'RNA': 33}
          Modifications used: {'3*END': 1, 'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 12, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 11, 'rna3p': 21}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 11
          Unusual residues: {' MG': 2, 'POP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 229
          Classifications: {'water': 229}
          Link IDs: {None: 228}
    Chain: "C"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 53
          Classifications: {'water': 53}
          Link IDs: {None: 52}
    Chain: "G"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "M"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
    Chain: "B"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 261
          Classifications: {'water': 261}
          Link IDs: {None: 260}
    Chain: "T"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 84
          Classifications: {'water': 84}
          Link IDs: {None: 83}
  Residues with excluded nonbonded symmetry interactions: 9
    residue:
      pdb=" N  ALYS A 378 " occ=0.50
      ... (42 atoms not shown)
      pdb=" HZ3BLYS A 378 " occ=0.50
    residue:
      pdb=" N  AILE A 465 " occ=0.50
      ... (36 atoms not shown)
      pdb="HD13BILE A 465 " occ=0.50
    residue:
      pdb=" N  AARG C  46 " occ=0.50
      ... (46 atoms not shown)
      pdb="HH22BARG C  46 " occ=0.50
    residue:
      pdb=" N  AMET C  50 " occ=0.50
      ... (32 atoms not shown)
      pdb=" HE3BMET C  50 " occ=0.50
    residue:
      pdb=" N  AASN C 148 " occ=0.40
      ... (26 atoms not shown)
      pdb="HD22BASN C 148 " occ=0.60
    residue:
      pdb=" N  AILE B 322 " occ=0.50
      ... (36 atoms not shown)
      pdb="HD13BILE B 322 " occ=0.50
    residue:
      pdb=" N  AARG B 334 " occ=0.50
      ... (46 atoms not shown)
      pdb="HH22BARG B 334 " occ=0.50
    residue:
      pdb=" N  ALEU B 337 " occ=0.50
      ... (36 atoms not shown)
      pdb="HD23BLEU B 337 " occ=0.50
    residue:
      pdb=" N  AARG B 350 " occ=0.60
      ... (46 atoms not shown)
      pdb="HH22BARG B 350 " occ=0.40
  Time building chain proxies: 9.11, per 1000 atoms: 0.30
  Number of scatterers: 29875
  At special positions: 0
  Unit cell: (95.63, 102.2, 142.35, 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)
     S     103     16.00
     P      49     15.00
     Mg      3     11.99
     O    3600      8.00
     N    2590      7.00
     C    9186      6.00
     H   14344      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.75
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3262

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 16 sheets defined
      53.8% alpha, 12.9% beta
      12 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 6.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 9
    Processing helix  chain 'A' and resid 10 through 23
    Processing helix  chain 'A' and resid 31 through 50
    Processing helix  chain 'A' and resid 83 through 99
    Processing helix  chain 'A' and resid 126 through 139
    Processing helix  chain 'A' and resid 158 through 160
      No H-bonds generated for 'chain 'A' and resid 158 through 160'
    Processing helix  chain 'A' and resid 164 through 185
    Processing helix  chain 'A' and resid 187 through 194
    Processing helix  chain 'A' and resid 195 through 199
      removed outlier: 3.786A  pdb=" N   GLU A 199 " --> pdb=" O   ARG A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 217
    Processing helix  chain 'A' and resid 225 through 235
    Processing helix  chain 'A' and resid 240 through 249
    Processing helix  chain 'A' and resid 302 through 313
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.759A  pdb=" N   TYR A 334 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 370
    Processing helix  chain 'A' and resid 380 through 385
    Processing helix  chain 'A' and resid 405 through 416
      removed outlier: 3.593A  pdb=" N   GLU A 416 " --> pdb=" O   ASN A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 452
    Processing helix  chain 'A' and resid 453 through 476
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.632A  pdb=" N   GLU A 538 " --> pdb=" O   HIS A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 580
    Processing helix  chain 'A' and resid 582 through 604
      removed outlier: 3.981A  pdb=" N   LEU A 586 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN A 591 " --> pdb=" O   GLN A 587 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL A 602 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 614
    Processing helix  chain 'A' and resid 632 through 650
    Processing helix  chain 'A' and resid 652 through 674
      removed outlier: 3.868A  pdb=" N   LYS A 664 " --> pdb=" O   ALA A 660 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 665 " --> pdb=" O   GLU A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 692
    Processing helix  chain 'A' and resid 697 through 715
    Processing helix  chain 'C' and resid 2 through 13
    Processing helix  chain 'C' and resid 13 through 23
    Processing helix  chain 'C' and resid 24 through 37
      removed outlier: 3.827A  pdb=" N   ALA C  29 " --> pdb=" O   VAL C  25 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ILE C  30 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLY C  37 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 51
    Processing helix  chain 'C' and resid 62 through 67
    Processing helix  chain 'C' and resid 92 through 103
      removed outlier: 3.747A  pdb=" N   VAL C  96 " --> pdb=" O   SER C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 115
    Processing helix  chain 'C' and resid 115 through 127
    Processing helix  chain 'C' and resid 155 through 168
    Processing helix  chain 'C' and resid 169 through 172
      removed outlier: 3.660A  pdb=" N   VAL C 172 " --> pdb=" O   PRO C 169 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 169 through 172'
    Processing helix  chain 'C' and resid 179 through 193
    Processing helix  chain 'C' and resid 199 through 212
    Processing helix  chain 'C' and resid 225 through 230
    Processing helix  chain 'C' and resid 231 through 236
    Processing helix  chain 'B' and resid 5 through 11
    Processing helix  chain 'B' and resid 13 through 22
      removed outlier: 5.683A  pdb=" N   SER B  19 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 50
      removed outlier: 3.512A  pdb=" N   SER B  50 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 99
    Processing helix  chain 'B' and resid 101 through 117
    Processing helix  chain 'B' and resid 118 through 125
    Processing helix  chain 'B' and resid 138 through 153
    Processing helix  chain 'B' and resid 156 through 161
    Processing helix  chain 'B' and resid 162 through 174
    Processing helix  chain 'B' and resid 214 through 222
    Processing helix  chain 'B' and resid 245 through 265
      removed outlier: 4.101A  pdb=" N   GLY B 250 " --> pdb=" O   MET B 246 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   PHE B 251 " --> pdb=" O   GLN B 247 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS B 265 " --> pdb=" O   SER B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 293
    Processing helix  chain 'B' and resid 308 through 313
    Processing helix  chain 'B' and resid 314 through 326
    Processing helix  chain 'B' and resid 330 through 346
      removed outlier: 4.558A  pdb=" N   ALA B 340 " --> pdb=" O   VAL B 336 " (cutoff:3.500A)
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 369 through 373
    Processing helix  chain 'B' and resid 377 through 381
      removed outlier: 4.113A  pdb=" N   TYR B 380 " --> pdb=" O   ASP B 377 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE B 381 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 377 through 381'
    Processing helix  chain 'B' and resid 382 through 393
    Processing helix  chain 'B' and resid 412 through 426
      removed outlier: 3.527A  pdb=" N   SER B 416 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 433
    Processing helix  chain 'B' and resid 455 through 473
    Processing helix  chain 'B' and resid 504 through 512
      removed outlier: 3.537A  pdb=" N   MET B 507 " --> pdb=" O   ASN B 504 " (cutoff:3.500A)
      Proline residue:  B 510  - end of helix
    Processing helix  chain 'B' and resid 518 through 537
    Processing helix  chain 'B' and resid 540 through 559
    Processing helix  chain 'B' and resid 572 through 583
    Processing helix  chain 'B' and resid 585 through 589
    Processing helix  chain 'B' and resid 590 through 594
    Processing helix  chain 'B' and resid 600 through 604
      removed outlier: 3.865A  pdb=" N   LEU B 604 " --> pdb=" O   ILE B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 612
    Processing helix  chain 'B' and resid 613 through 616
    Processing helix  chain 'B' and resid 617 through 625
    Processing helix  chain 'B' and resid 685 through 700
      removed outlier: 3.647A  pdb=" N   TYR B 689 " --> pdb=" O   ASP B 685 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 704
      removed outlier: 4.300A  pdb=" N   SER B 704 " --> pdb=" O   PRO B 701 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 701 through 704'
    Processing helix  chain 'B' and resid 713 through 733
    Processing helix  chain 'B' and resid 736 through 756
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.407A  pdb=" N   PHE A 117 " --> pdb=" O   HIS A 144 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   HIS A 146 " --> pdb=" O   PHE A 117 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   GLU A 119 " --> pdb=" O   HIS A 146 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   PHE A 148 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   GLY A 121 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259
    Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293
      removed outlier: 7.293A  pdb=" N   TYR A 501 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   GLY A 555 " --> pdb=" O   ARG A 551 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   ARG A 551 " --> pdb=" O   GLY A 555 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   VAL A 557 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   LEU A 549 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ARG A 559 " --> pdb=" O   ASP A 547 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ASP A 547 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   MET A 561 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL A 542 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   GLY A 546 " --> pdb=" O   GLU A 319 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   GLU A 319 " --> pdb=" O   GLY A 546 " (cutoff:3.500A)
      removed outlier: 8.922A  pdb=" N   MET A 548 " --> pdb=" O   TRP A 317 " (cutoff:3.500A)
      removed outlier: 9.769A  pdb=" N   TRP A 317 " --> pdb=" O   MET A 548 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293
      removed outlier: 5.291A  pdb=" N   THR A 498 " --> pdb=" O   CYS A 489 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   CYS A 489 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
      removed outlier: 5.383A  pdb=" N   LEU A 500 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   SER A 487 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   GLY A 502 " --> pdb=" O   MET A 485 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLN A 481 " --> pdb=" O   LYS A 506 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   PHE A 480 " --> pdb=" O   MET A 360 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   LYS A 358 " --> pdb=" O   LEU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 378
      removed outlier: 5.822A  pdb=" N   GLU A 377 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   GLN B 367 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631
      removed outlier: 6.128A  pdb=" N   GLY A 631 " --> pdb=" O   PRO A 620 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 80
      removed outlier: 4.474A  pdb=" N   ILE B 667 " --> pdb=" O   THR C  58 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 135
      removed outlier: 4.702A  pdb=" N   MET C 243 " --> pdb=" O   GLY C 131 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   VAL C 133 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLU C 241 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 148
      removed outlier: 6.513A  pdb=" N   LYS C 214 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 57
    Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 130
    Processing sheet with id=AB4, first strand: chain 'B' and resid 178 through 183
    Processing sheet with id=AB5, first strand: chain 'B' and resid 187 through 188
    Processing sheet with id=AB6, first strand: chain 'B' and resid 240 through 244
      removed outlier: 6.891A  pdb=" N   LEU B 224 " --> pdb=" O  AARG B 350 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 492

    742 hydrogen bonds defined for protein.
    2053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      33 hydrogen bonds
      66 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 8.16

  Time building geometry restraints manager: 3.92 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 14315
        1.03 -     1.23: 45
        1.23 -     1.42: 6422
        1.42 -     1.62: 8649
        1.62 -     1.81: 177
  Bond restraints: 29608
  Sorted by residual:
  bond pdb=" O   POP B 803 "
       pdb=" P2  POP B 803 "
    ideal  model  delta    sigma   weight residual
    1.661  1.611  0.050 2.00e-02 2.50e+03 6.32e+00
  bond pdb=" O   POP B 803 "
       pdb=" P1  POP B 803 "
    ideal  model  delta    sigma   weight residual
    1.660  1.612  0.048 2.00e-02 2.50e+03 5.67e+00
  bond pdb=" O1  POP B 803 "
       pdb=" P1  POP B 803 "
    ideal  model  delta    sigma   weight residual
    1.531  1.507  0.024 2.00e-02 2.50e+03 1.42e+00
  bond pdb=" C   MET A 441 "
       pdb=" O   MET A 441 "
    ideal  model  delta    sigma   weight residual
    1.236  1.250 -0.013 1.15e-02 7.56e+03 1.29e+00
  bond pdb=" O2  POP B 803 "
       pdb=" P1  POP B 803 "
    ideal  model  delta    sigma   weight residual
    1.531  1.509  0.022 2.00e-02 2.50e+03 1.25e+00
  ... (remaining 29603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.59: 53471
        3.59 -     7.18: 23
        7.18 -    10.77: 1
       10.77 -    14.36: 0
       14.36 -    17.94: 1
  Bond angle restraints: 53496
  Sorted by residual:
  angle pdb=" P1  POP B 803 "
        pdb=" O   POP B 803 "
        pdb=" P2  POP B 803 "
      ideal   model   delta    sigma   weight residual
     139.66  121.72   17.94 3.00e+00 1.11e-01 3.58e+01
  angle pdb=" N   ILE A 323 "
        pdb=" CA  ILE A 323 "
        pdb=" C   ILE A 323 "
      ideal   model   delta    sigma   weight residual
     113.53  110.32    3.21 9.80e-01 1.04e+00 1.07e+01
  angle pdb=" CA  TYR B 557 "
        pdb=" CB  TYR B 557 "
        pdb=" CG  TYR B 557 "
      ideal   model   delta    sigma   weight residual
     113.90  109.09    4.81 1.80e+00 3.09e-01 7.15e+00
  angle pdb=" O   POP B 803 "
        pdb=" P1  POP B 803 "
        pdb=" O2  POP B 803 "
      ideal   model   delta    sigma   weight residual
     102.11  109.84   -7.73 3.00e+00 1.11e-01 6.65e+00
  angle pdb=" O4'   A T   7 "
        pdb=" C1'   A T   7 "
        pdb=" N9    A T   7 "
      ideal   model   delta    sigma   weight residual
     108.20  111.95   -3.75 1.50e+00 4.44e-01 6.26e+00
  ... (remaining 53491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 12395
       17.76 -    35.51: 1009
       35.51 -    53.27: 380
       53.27 -    71.03: 140
       71.03 -    88.79: 44
  Dihedral angle restraints: 13968
    sinusoidal: 8089
      harmonic: 5879
  Sorted by residual:
  dihedral pdb=" CA  ILE B 302 "
           pdb=" C   ILE B 302 "
           pdb=" N   THR B 303 "
           pdb=" CA  THR B 303 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.46   20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  ARG B 602 "
           pdb=" C   ARG B 602 "
           pdb=" N   ASN B 603 "
           pdb=" CA  ASN B 603 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.10  -18.90     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  TYR A 540 "
           pdb=" C   TYR A 540 "
           pdb=" N   CYS A 541 "
           pdb=" CA  CYS A 541 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.25   18.75     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 13965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1603
       0.032 -    0.064: 505
       0.064 -    0.096: 127
       0.096 -    0.129: 57
       0.129 -    0.161: 9
  Chirality restraints: 2301
  Sorted by residual:
  chirality pdb=" C1'   A T   4 "
            pdb=" O4'   A T   4 "
            pdb=" C2'   A T   4 "
            pdb=" N9    A T   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.30    0.16 2.00e-01 2.50e+01 6.45e-01
  chirality pdb=" C1'   A T   7 "
            pdb=" O4'   A T   7 "
            pdb=" C2'   A T   7 "
            pdb=" N9    A T   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.29    0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  ILE A 302 "
            pdb=" N   ILE A 302 "
            pdb=" C   ILE A 302 "
            pdb=" CB  ILE A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 2298 not shown)

  Planarity restraints: 4198
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A T   4 "    0.033 2.00e-02 2.50e+03   1.31e-02 5.55e+00
        pdb=" N9    A T   4 "   -0.031 2.00e-02 2.50e+03
        pdb=" C8    A T   4 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7    A T   4 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A T   4 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A T   4 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A T   4 "    0.009 2.00e-02 2.50e+03
        pdb=" N1    A T   4 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A T   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A T   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    A T   4 "   -0.004 2.00e-02 2.50e+03
        pdb=" H8    A T   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" H2    A T   4 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A T   7 "    0.027 2.00e-02 2.50e+03   1.12e-02 4.06e+00
        pdb=" N9    A T   7 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8    A T   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A T   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A T   7 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A T   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A T   7 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    A T   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A T   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A T   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A T   7 "   -0.006 2.00e-02 2.50e+03
        pdb=" H8    A T   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" H2    A T   7 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 594 "    0.008 2.00e-02 2.50e+03   1.57e-02 2.46e+00
        pdb=" C   SER A 594 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   SER A 594 "    0.010 2.00e-02 2.50e+03
        pdb=" N   MET A 595 "    0.009 2.00e-02 2.50e+03
  ... (remaining 4195 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 2129
        2.20 -     2.80: 60893
        2.80 -     3.40: 89618
        3.40 -     4.00: 121528
        4.00 -     4.60: 182220
  Nonbonded interactions: 456388
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 427 "
            pdb=" H   GLU A 427 "
     model   vdw
     1.600 2.450
  nonbonded pdb=" OE2 GLU B 519 "
            pdb="HH12 ARG B 572 "
     model   vdw
     1.650 2.450
  nonbonded pdb=" H   HIS A 326 "
            pdb=" OD1 ASN A 331 "
     model   vdw
     1.655 2.450
  nonbonded pdb=" HZ2 LYS A 362 "
            pdb=" O   ASP A 478 "
     model   vdw
     1.655 2.450
  nonbonded pdb=" HE  ARG A 583 "
            pdb=" O   PHE B 512 "
     model   vdw
     1.660 2.450
  ... (remaining 456383 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=0.40 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.540
  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:             0.210
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     40.280
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
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      :  0.002   0.050  15264  Z= 0.124
  Angle     :  0.496  17.945  20821  Z= 0.262
  Chirality :  0.037   0.161   2301
  Planarity :  0.003   0.035   2519
  Dihedral  : 17.616  88.787   6146
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.25 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.20), residues: 1719
  helix:  1.87 (0.18), residues: 846
  sheet: -0.27 (0.36), residues: 189
  loop :  0.30 (0.24), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 144 
 TYR   0.023   0.001   TYR B 557 
 PHE   0.013   0.001   PHE B 551 
 TRP   0.015   0.002   TRP C  49 
 HIS   0.003   0.001   HIS B 664 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (15264)
  covalent geometry    : angle       0.49605 (20821)
  hydrogen bonds       : bond        0.12388 (  771)
  hydrogen bonds       : angle       5.53299 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 238
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7371 (mt-10)
REVERT: A   84 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7602 (ttt90)
REVERT: A  394 ASP cc_start: 0.8181 (t70) cc_final: 0.7971 (t0)
REVERT: C   11 MET cc_start: 0.8251 (mmm) cc_final: 0.7700 (mmm)
REVERT: C   17 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7577 (ttp80)
REVERT: C  146 ASP cc_start: 0.8176 (m-30) cc_final: 0.7894 (m-30)
REVERT: C  160 GLN cc_start: 0.7932 (mt0) cc_final: 0.7004 (tp-100)
REVERT: C  176 ILE cc_start: 0.8099 (tt) cc_final: 0.7812 (pp)
REVERT: C  191 LYS cc_start: 0.8066 (tttt) cc_final: 0.7694 (tmtt)
REVERT: B  104 GLU cc_start: 0.8141 (tt0) cc_final: 0.7897 (mp0)
REVERT: B  116 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8261 (mp10)
REVERT: B  120 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8565 (p0)
REVERT: B  159 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7419 (mm-30)
REVERT: B  179 MET cc_start: 0.8584 (tpt) cc_final: 0.8296 (mmm)
REVERT: B  227 MET cc_start: 0.8243 (mpp) cc_final: 0.8025 (mpp)
REVERT: B  287 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7724 (ttm-80)
REVERT: B  445 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8613 (p0)
REVERT: B  569 GLN cc_start: 0.8609 (mm110) cc_final: 0.8388 (mm110)
REVERT: B  602 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7915 (ttp-110)
REVERT: B  691 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7295 (mttp)
REVERT: B  707 ARG cc_start: 0.8024 (tmm160) cc_final: 0.7746 (ttp80)
  outliers start: 12
  outliers final: 2
  residues processed: 250
  average time/residue: 1.9819
  time to fit residues: 531.6455
Evaluate side-chains
  209 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 204
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  445 ASP
Chi-restraints excluded: chain B residue  602 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 614 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.160788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.118556 restraints weight = 67815.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.07
r_work: 0.3116 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.1067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15264  Z= 0.201
  Angle     :  0.586   5.937  20821  Z= 0.319
  Chirality :  0.040   0.188   2301
  Planarity :  0.005   0.050   2519
  Dihedral  : 13.529  84.448   2603
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 11.77 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.20), residues: 1719
  helix:  1.60 (0.17), residues: 850
  sheet: -0.40 (0.37), residues: 188
  loop :  0.25 (0.24), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 279 
 TYR   0.030   0.002   TYR B 557 
 PHE   0.018   0.002   PHE B 551 
 TRP   0.020   0.002   TRP B 309 
 HIS   0.005   0.001   HIS A 713 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (15264)
  covalent geometry    : angle       0.58560 (20821)
  hydrogen bonds       : bond        0.06630 (  771)
  hydrogen bonds       : angle       5.04792 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 205
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7335 (mt-10)
REVERT: A   84 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7693 (ttt90)
REVERT: A  204 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7839 (ttm170)
REVERT: A  394 ASP cc_start: 0.8174 (t70) cc_final: 0.7974 (t0)
REVERT: A  493 GLU cc_start: 0.8170 (mp0) cc_final: 0.7750 (mp0)
REVERT: C   11 MET cc_start: 0.8235 (mmm) cc_final: 0.7627 (mmm)
REVERT: C  146 ASP cc_start: 0.8297 (m-30) cc_final: 0.7995 (m-30)
REVERT: C  160 GLN cc_start: 0.7875 (mt0) cc_final: 0.7037 (tp-100)
REVERT: C  176 ILE cc_start: 0.8098 (tt) cc_final: 0.7839 (pp)
REVERT: C  191 LYS cc_start: 0.8068 (tttt) cc_final: 0.7692 (tmtt)
REVERT: B  159 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7484 (mm-30)
REVERT: B  179 MET cc_start: 0.8607 (tpt) cc_final: 0.8268 (mmm)
REVERT: B  430 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8320 (pttp)
REVERT: B  691 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7304 (mttp)
REVERT: B  707 ARG cc_start: 0.8058 (tmm160) cc_final: 0.7775 (ttp80)
  outliers start: 14
  outliers final: 4
  residues processed: 214
  average time/residue: 2.0039
  time to fit residues: 459.8224
Evaluate side-chains
  196 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 190
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ARG
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  430 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 171 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 123 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 80 optimal weight:    0.5980
   chunk 165 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 614 ASN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.161725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.118620 restraints weight = 63519.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.94
r_work: 0.3154 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15264  Z= 0.135
  Angle     :  0.518   4.994  20821  Z= 0.280
  Chirality :  0.038   0.179   2301
  Planarity :  0.004   0.031   2519
  Dihedral  : 13.345  85.770   2592
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 12.16 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.20), residues: 1719
  helix:  1.69 (0.17), residues: 856
  sheet: -0.37 (0.37), residues: 186
  loop :  0.22 (0.24), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 721 
 TYR   0.024   0.002   TYR B 557 
 PHE   0.014   0.001   PHE B 551 
 TRP   0.015   0.002   TRP C  49 
 HIS   0.004   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (15264)
  covalent geometry    : angle       0.51816 (20821)
  hydrogen bonds       : bond        0.05599 (  771)
  hydrogen bonds       : angle       4.80811 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 198
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7303 (mt-10)
REVERT: A   84 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7653 (ttt90)
REVERT: C  146 ASP cc_start: 0.8209 (m-30) cc_final: 0.7910 (m-30)
REVERT: C  160 GLN cc_start: 0.7822 (mt0) cc_final: 0.6943 (tp-100)
REVERT: C  176 ILE cc_start: 0.8096 (tt) cc_final: 0.7853 (pp)
REVERT: C  191 LYS cc_start: 0.8069 (tttt) cc_final: 0.7720 (tmtt)
REVERT: B  159 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7494 (mm-30)
REVERT: B  179 MET cc_start: 0.8597 (tpt) cc_final: 0.8306 (mmm)
REVERT: B  430 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8345 (pttp)
REVERT: B  691 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7287 (mttp)
REVERT: B  707 ARG cc_start: 0.8078 (tmm160) cc_final: 0.7773 (ttp80)
  outliers start: 7
  outliers final: 3
  residues processed: 203
  average time/residue: 1.9408
  time to fit residues: 422.9980
Evaluate side-chains
  193 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 189
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  430 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0050
   chunk 86 optimal weight:    8.9990
   chunk 122 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 169 optimal weight:    4.9990
   chunk 138 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    2.5800

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 614 ASN
C 151 HIS
B 569 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.158799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.115744 restraints weight = 63188.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.85
r_work: 0.3113 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  15264  Z= 0.221
  Angle     :  0.613   6.239  20821  Z= 0.332
  Chirality :  0.041   0.190   2301
  Planarity :  0.005   0.056   2519
  Dihedral  : 13.497  86.733   2592
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 11.51 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.20), residues: 1719
  helix:  1.42 (0.17), residues: 855
  sheet: -0.43 (0.37), residues: 188
  loop :  0.11 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 144 
 TYR   0.030   0.002   TYR B 557 
 PHE   0.019   0.002   PHE B 551 
 TRP   0.020   0.003   TRP B 309 
 HIS   0.007   0.002   HIS B 664 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (15264)
  covalent geometry    : angle       0.61263 (20821)
  hydrogen bonds       : bond        0.06862 (  771)
  hydrogen bonds       : angle       5.06296 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 192
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7333 (mt-10)
REVERT: A   84 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7642 (ttt90)
REVERT: C  146 ASP cc_start: 0.8323 (m-30) cc_final: 0.8014 (m-30)
REVERT: C  160 GLN cc_start: 0.7871 (mt0) cc_final: 0.7031 (tp-100)
REVERT: C  191 LYS cc_start: 0.8072 (tttt) cc_final: 0.7709 (tmtt)
REVERT: B  120 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8567 (p0)
REVERT: B  159 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7490 (mm-30)
REVERT: B  179 MET cc_start: 0.8642 (tpt) cc_final: 0.8264 (mmm)
REVERT: B  430 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8373 (pttp)
REVERT: B  691 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7311 (mttp)
REVERT: B  698 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7298 (mtmm)
REVERT: B  707 ARG cc_start: 0.8078 (tmm160) cc_final: 0.7789 (ttp80)
  outliers start: 10
  outliers final: 4
  residues processed: 198
  average time/residue: 1.8871
  time to fit residues: 401.9087
Evaluate side-chains
  198 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 191
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  430 LYS
Chi-restraints excluded: chain B residue  698 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 133 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 130 optimal weight:    0.0970
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 614 ASN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.160536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.117316 restraints weight = 61835.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.89
r_work: 0.3138 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15264  Z= 0.151
  Angle     :  0.540   5.350  20821  Z= 0.291
  Chirality :  0.038   0.173   2301
  Planarity :  0.004   0.036   2519
  Dihedral  : 13.412  88.022   2592
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 11.90 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.20), residues: 1719
  helix:  1.60 (0.17), residues: 849
  sheet: -0.42 (0.38), residues: 186
  loop :  0.08 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 721 
 TYR   0.025   0.002   TYR B 557 
 PHE   0.015   0.001   PHE B 551 
 TRP   0.016   0.002   TRP B 309 
 HIS   0.004   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (15264)
  covalent geometry    : angle       0.53965 (20821)
  hydrogen bonds       : bond        0.05840 (  771)
  hydrogen bonds       : angle       4.85727 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 194
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7328 (mt-10)
REVERT: A   84 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7646 (ttt90)
REVERT: C  146 ASP cc_start: 0.8289 (m-30) cc_final: 0.7972 (m-30)
REVERT: C  160 GLN cc_start: 0.7829 (mt0) cc_final: 0.6991 (tp-100)
REVERT: C  191 LYS cc_start: 0.8073 (tttt) cc_final: 0.7726 (tmtt)
REVERT: B  159 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7489 (mm-30)
REVERT: B  179 MET cc_start: 0.8607 (tpt) cc_final: 0.8275 (mmm)
REVERT: B  430 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8376 (pttp)
REVERT: B  691 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7295 (mttp)
REVERT: B  707 ARG cc_start: 0.8071 (tmm160) cc_final: 0.7775 (ttp80)
  outliers start: 6
  outliers final: 4
  residues processed: 199
  average time/residue: 1.9512
  time to fit residues: 417.2018
Evaluate side-chains
  195 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 190
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  430 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0010
   chunk 15 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 142 optimal weight:    0.8980
   chunk 171 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 614 ASN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.161361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.119473 restraints weight = 70851.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.01
r_work: 0.3138 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15264  Z= 0.135
  Angle     :  0.520   5.544  20821  Z= 0.280
  Chirality :  0.038   0.172   2301
  Planarity :  0.004   0.031   2519
  Dihedral  : 13.328  88.359   2592
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 12.29 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.20), residues: 1719
  helix:  1.72 (0.18), residues: 849
  sheet: -0.45 (0.38), residues: 186
  loop :  0.12 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 721 
 TYR   0.024   0.002   TYR B 557 
 PHE   0.014   0.001   PHE B 551 
 TRP   0.016   0.002   TRP C  49 
 HIS   0.004   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (15264)
  covalent geometry    : angle       0.52009 (20821)
  hydrogen bonds       : bond        0.05464 (  771)
  hydrogen bonds       : angle       4.74646 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 196
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7356 (mt-10)
REVERT: A   84 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7685 (ttt90)
REVERT: A  113 LYS cc_start: 0.7970 (tttm) cc_final: 0.7730 (ttpp)
REVERT: C   18 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7179 (mm-30)
REVERT: C  146 ASP cc_start: 0.8198 (m-30) cc_final: 0.7901 (m-30)
REVERT: C  160 GLN cc_start: 0.7837 (mt0) cc_final: 0.7003 (tp-100)
REVERT: C  191 LYS cc_start: 0.8070 (tttt) cc_final: 0.7719 (tmtt)
REVERT: B  120 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8583 (p0)
REVERT: B  159 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7554 (mm-30)
REVERT: B  179 MET cc_start: 0.8614 (tpt) cc_final: 0.8290 (mmm)
REVERT: B  430 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8378 (pttp)
REVERT: B  691 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7291 (mttp)
REVERT: B  707 ARG cc_start: 0.8074 (tmm160) cc_final: 0.7776 (ttp80)
  outliers start: 7
  outliers final: 4
  residues processed: 201
  average time/residue: 1.9864
  time to fit residues: 428.0116
Evaluate side-chains
  198 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 192
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  430 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 137 optimal weight:    0.3980
   chunk 170 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 172 optimal weight:    5.9990
   chunk 167 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 128 optimal weight:    0.5980
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 614 ASN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.159564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.116768 restraints weight = 65780.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.90
r_work: 0.3123 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15264  Z= 0.185
  Angle     :  0.574   5.731  20821  Z= 0.310
  Chirality :  0.039   0.184   2301
  Planarity :  0.004   0.046   2519
  Dihedral  : 13.433  88.262   2592
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.09 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.20), residues: 1719
  helix:  1.55 (0.17), residues: 849
  sheet: -0.49 (0.37), residues: 188
  loop :  0.08 (0.23), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 496 
 TYR   0.028   0.002   TYR B 557 
 PHE   0.018   0.002   PHE B 551 
 TRP   0.018   0.002   TRP B 309 
 HIS   0.005   0.001   HIS B 664 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (15264)
  covalent geometry    : angle       0.57381 (20821)
  hydrogen bonds       : bond        0.06315 (  771)
  hydrogen bonds       : angle       4.92228 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 193
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7356 (mt-10)
REVERT: A   84 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7645 (ttt90)
REVERT: C   18 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7197 (mm-30)
REVERT: C  146 ASP cc_start: 0.8257 (m-30) cc_final: 0.7948 (m-30)
REVERT: C  160 GLN cc_start: 0.7850 (mt0) cc_final: 0.7002 (tp-100)
REVERT: C  191 LYS cc_start: 0.8057 (tttt) cc_final: 0.7711 (tmtt)
REVERT: B  120 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8575 (p0)
REVERT: B  159 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7525 (mm-30)
REVERT: B  179 MET cc_start: 0.8632 (tpt) cc_final: 0.8275 (mmm)
REVERT: B  430 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8371 (pttp)
REVERT: B  691 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7255 (mttp)
REVERT: B  707 ARG cc_start: 0.8085 (tmm160) cc_final: 0.7784 (ttp80)
  outliers start: 10
  outliers final: 6
  residues processed: 200
  average time/residue: 1.9741
  time to fit residues: 424.5312
Evaluate side-chains
  199 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 191
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  430 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 22 optimal weight:    0.1980
   chunk 70 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 78 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 170 optimal weight:    2.9990
   chunk 159 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 614 ASN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.162385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.118928 restraints weight = 63868.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.03
r_work: 0.3158 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  15264  Z= 0.117
  Angle     :  0.502   5.837  20821  Z= 0.269
  Chirality :  0.037   0.177   2301
  Planarity :  0.003   0.031   2519
  Dihedral  : 13.285  88.829   2592
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 12.61 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.20), residues: 1719
  helix:  1.81 (0.18), residues: 849
  sheet: -0.49 (0.38), residues: 186
  loop :  0.10 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 721 
 TYR   0.022   0.001   TYR B 557 
 PHE   0.012   0.001   PHE B 551 
 TRP   0.017   0.002   TRP C  49 
 HIS   0.003   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (15264)
  covalent geometry    : angle       0.50232 (20821)
  hydrogen bonds       : bond        0.05067 (  771)
  hydrogen bonds       : angle       4.66767 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 195
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7347 (mt-10)
REVERT: A   84 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7664 (ttt90)
REVERT: C   18 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7141 (mm-30)
REVERT: C  146 ASP cc_start: 0.8145 (m-30) cc_final: 0.7858 (m-30)
REVERT: C  160 GLN cc_start: 0.7812 (mt0) cc_final: 0.6924 (tp-100)
REVERT: C  191 LYS cc_start: 0.8069 (tttt) cc_final: 0.7746 (tmtt)
REVERT: B  159 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7555 (mm-30)
REVERT: B  179 MET cc_start: 0.8604 (tpt) cc_final: 0.8292 (mmm)
REVERT: B  445 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8595 (p0)
REVERT: B  691 LYS cc_start: 0.7682 (mtpt) cc_final: 0.7282 (mttp)
REVERT: B  707 ARG cc_start: 0.8072 (tmm160) cc_final: 0.7766 (ttp80)
  outliers start: 5
  outliers final: 3
  residues processed: 198
  average time/residue: 1.9235
  time to fit residues: 409.2390
Evaluate side-chains
  195 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 191
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain B residue  445 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 130 optimal weight:    0.5980
   chunk 12 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 169 optimal weight:    8.9990
   chunk 116 optimal weight:    4.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
B 284 ASN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.160681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.117662 restraints weight = 61081.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.73
r_work: 0.3148 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3018
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15264  Z= 0.155
  Angle     :  0.542   6.076  20821  Z= 0.292
  Chirality :  0.038   0.170   2301
  Planarity :  0.004   0.037   2519
  Dihedral  : 13.355  89.200   2592
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 12.35 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.20), residues: 1719
  helix:  1.72 (0.18), residues: 849
  sheet: -0.51 (0.37), residues: 186
  loop :  0.10 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 706 
 TYR   0.026   0.002   TYR B 557 
 PHE   0.016   0.001   PHE B 551 
 TRP   0.016   0.002   TRP B 309 
 HIS   0.004   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (15264)
  covalent geometry    : angle       0.54153 (20821)
  hydrogen bonds       : bond        0.05763 (  771)
  hydrogen bonds       : angle       4.78409 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 191
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7389 (mt-10)
REVERT: A   84 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7601 (ttt90)
REVERT: C   18 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7135 (mm-30)
REVERT: C  146 ASP cc_start: 0.8186 (m-30) cc_final: 0.7884 (m-30)
REVERT: C  160 GLN cc_start: 0.7816 (mt0) cc_final: 0.6968 (tp-100)
REVERT: C  191 LYS cc_start: 0.8055 (tttt) cc_final: 0.7710 (tmtt)
REVERT: B  159 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7515 (mm-30)
REVERT: B  179 MET cc_start: 0.8612 (tpt) cc_final: 0.8267 (mmm)
REVERT: B  372 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7972 (ptm)
REVERT: B  430 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8403 (pttp)
REVERT: B  691 LYS cc_start: 0.7661 (mtpt) cc_final: 0.7242 (mttp)
REVERT: B  707 ARG cc_start: 0.8066 (tmm160) cc_final: 0.7753 (ttp80)
  outliers start: 7
  outliers final: 4
  residues processed: 195
  average time/residue: 1.9296
  time to fit residues: 404.7096
Evaluate side-chains
  196 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 190
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  430 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 127 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 131 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 137 optimal weight:    0.8980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 614 ASN
B 284 ASN
B 569 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.160301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.117837 restraints weight = 70262.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.97
r_work: 0.3127 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15264  Z= 0.160
  Angle     :  0.551   6.205  20821  Z= 0.297
  Chirality :  0.039   0.172   2301
  Planarity :  0.004   0.040   2519
  Dihedral  : 13.407  90.626   2592
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 12.48 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.20), residues: 1719
  helix:  1.64 (0.17), residues: 849
  sheet: -0.54 (0.37), residues: 188
  loop :  0.08 (0.23), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 706 
 TYR   0.026   0.002   TYR B 557 
 PHE   0.016   0.002   PHE B 551 
 TRP   0.017   0.002   TRP B 309 
 HIS   0.005   0.001   HIS B 664 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (15264)
  covalent geometry    : angle       0.55132 (20821)
  hydrogen bonds       : bond        0.05908 (  771)
  hydrogen bonds       : angle       4.83683 ( 2119)

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

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

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3438 Ramachandran restraints generated.
    1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 193
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7395 (mt-10)
REVERT: A   84 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7660 (ttt90)
REVERT: C   18 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7160 (mm-30)
REVERT: C  146 ASP cc_start: 0.8243 (m-30) cc_final: 0.7961 (m-30)
REVERT: C  160 GLN cc_start: 0.7852 (mt0) cc_final: 0.7005 (tp-100)
REVERT: C  191 LYS cc_start: 0.8055 (tttt) cc_final: 0.7700 (tmtt)
REVERT: B  159 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7535 (mm-30)
REVERT: B  179 MET cc_start: 0.8634 (tpt) cc_final: 0.8277 (mmm)
REVERT: B  372 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7995 (ptm)
REVERT: B  430 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8414 (pttp)
REVERT: B  691 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7267 (mttp)
REVERT: B  707 ARG cc_start: 0.8079 (tmm160) cc_final: 0.7757 (ttp80)
  outliers start: 6
  outliers final: 4
  residues processed: 196
  average time/residue: 1.9836
  time to fit residues: 417.3228
Evaluate side-chains
  198 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 192
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain C residue  217 PHE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  430 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 157 optimal weight:    2.9990
   chunk 121 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 166 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 154 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
B 284 ASN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.161279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.119455 restraints weight = 65698.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.79
r_work: 0.3155 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15264  Z= 0.137
  Angle     :  0.527   6.701  20821  Z= 0.283
  Chirality :  0.038   0.174   2301
  Planarity :  0.004   0.032   2519
  Dihedral  : 13.349  91.320   2592
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 12.42 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.20), residues: 1719
  helix:  1.74 (0.18), residues: 849
  sheet: -0.52 (0.37), residues: 186
  loop :  0.08 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 706 
 TYR   0.024   0.002   TYR B 557 
 PHE   0.014   0.001   PHE B 551 
 TRP   0.016   0.002   TRP B 309 
 HIS   0.004   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (15264)
  covalent geometry    : angle       0.52688 (20821)
  hydrogen bonds       : bond        0.05467 (  771)
  hydrogen bonds       : angle       4.73636 ( 2119)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15688.00 seconds
wall clock time: 265 minutes 16.10 seconds (15916.10 seconds total)