Starting phenix.real_space_refine
on Thu Feb 15 22:29:51 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/02_2024/8fhn_29096_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/02_2024/8fhn_29096.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/02_2024/8fhn_29096_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/02_2024/8fhn_29096_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/02_2024/8fhn_29096_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/02_2024/8fhn_29096.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/02_2024/8fhn_29096.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/02_2024/8fhn_29096_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/02_2024/8fhn_29096_updated.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.051
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       6      5.49       5
     S      80      5.16       5
     Cl      2      4.86       5
     C    8847      2.51       5
     N    2273      2.21       5
     O    2399      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  320": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  347": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  417": "OE1" <-> "OE2"
    Residue "A TYR  438": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  499": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  524": "OE1" <-> "OE2"
    Residue "A TYR  602": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  665": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  778": "OE1" <-> "OE2"
    Residue "A PHE  837": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  898": "OD1" <-> "OD2"
    Residue "A TYR  990": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  204": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  248": "OE1" <-> "OE2"
    Residue "B ASP  259": "OD1" <-> "OD2"
    Residue "B GLU  310": "OE1" <-> "OE2"
    Residue "B GLU  485": "OE1" <-> "OE2"
    Residue "B GLU  524": "OE1" <-> "OE2"
    Residue "B TYR  565": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  641": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  755": "OE1" <-> "OE2"
    Residue "B PHE  822": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  966": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  167": "OE1" <-> "OE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 13613
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 846, 6621
          Classifications: {'peptide': 846}
          Link IDs: {'PTRANS': 37, 'TRANS': 808}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 847, 6643
          Classifications: {'peptide': 847}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 36, 'TRANS': 810}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 237
          Classifications: {'peptide': 29}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 26}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'ATP': 1, 'XZF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'ATP': 1, 'XZF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.38, per 1000 atoms: 0.54
  Number of scatterers: 13613
  At special positions: 0
  Unit cell: (112.66, 141.9, 113.52, 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)
     Cl      2     17.00
     S      80     16.00
     P       6     15.00
     F       6      9.00
     O    2399      8.00
     N    2273      7.00
     C    8847      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 416 " - pdb=" SG  CYS A 421 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 436 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 416 " - pdb=" SG  CYS B 421 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 430 " - pdb=" SG  CYS B 436 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 5.44
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3172

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      74 helices and 3 sheets defined
      53.9% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 143 through 150
    Processing helix  chain 'A' and resid 154 through 157
      No H-bonds generated for 'chain 'A' and resid 154 through 157'
    Processing helix  chain 'A' and resid 159 through 194
      removed outlier: 6.925A  pdb=" N   ILE A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 9.195A  pdb=" N   VAL A 169 " --> pdb=" O   GLN A 165 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LEU A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   THR A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   VAL A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   THR A 182 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER A 193 " --> pdb=" O   ILE A 189 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   THR A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 211
      removed outlier: 3.599A  pdb=" N   SER A 210 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
      No H-bonds generated for 'chain 'A' and resid 213 through 216'
    Processing helix  chain 'A' and resid 220 through 249
      removed outlier: 3.982A  pdb=" N   ALA A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLY A 237 " --> pdb=" O   MET A 233 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLU A 248 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 276
      removed outlier: 3.689A  pdb=" N   ILE A 262 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 305
      removed outlier: 3.772A  pdb=" N   SER A 283 " --> pdb=" O   MET A 279 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LYS A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL A 287 " --> pdb=" O   SER A 283 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A 288 " --> pdb=" O   LYS A 284 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LEU A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 315
      removed outlier: 4.242A  pdb=" N   LYS A 315 " --> pdb=" O   ASP A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 327
    Processing helix  chain 'A' and resid 340 through 350
      removed outlier: 3.823A  pdb=" N   ILE A 346 " --> pdb=" O   GLY A 342 " (cutoff:3.500A)
      Proline residue:  A 349  - end of helix
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 367 through 395
      removed outlier: 3.630A  pdb=" N   ILE A 371 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
      Proline residue:  A 372  - end of helix
      removed outlier: 3.594A  pdb=" N   ALA A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   SER A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 423
    Processing helix  chain 'A' and resid 428 through 433
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 454 through 485
      removed outlier: 3.859A  pdb=" N   SER A 468 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA A 469 " --> pdb=" O   THR A 465 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA A 477 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   CYS A 482 " --> pdb=" O   LYS A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 495
    Processing helix  chain 'A' and resid 508 through 522
      removed outlier: 3.718A  pdb=" N   ILE A 522 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 535
    Processing helix  chain 'A' and resid 537 through 553
      removed outlier: 3.742A  pdb=" N   CYS A 547 " --> pdb=" O   ILE A 543 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR A 553 " --> pdb=" O   HIS A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 584
      removed outlier: 3.755A  pdb=" N   VAL A 578 " --> pdb=" O   ALA A 574 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   MET A 581 " --> pdb=" O   SER A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 606
      removed outlier: 3.730A  pdb=" N   LEU A 590 " --> pdb=" O   TRP A 586 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE A 591 " --> pdb=" O   TRP A 587 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 633
      removed outlier: 3.645A  pdb=" N   SER A 620 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   TYR A 621 " --> pdb=" O   GLN A 617 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ASN A 622 " --> pdb=" O   ALA A 618 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   TYR A 627 " --> pdb=" O   LEU A 623 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ASN A 632 " --> pdb=" O   SER A 628 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   GLU A 633 " --> pdb=" O   VAL A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 665
      removed outlier: 3.802A  pdb=" N   PHE A 661 " --> pdb=" O   ALA A 657 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   VAL A 662 " --> pdb=" O   LEU A 658 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   PHE A 665 " --> pdb=" O   PHE A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 702
    Processing helix  chain 'A' and resid 718 through 727
      removed outlier: 3.613A  pdb=" N   GLN A 722 " --> pdb=" O   ARG A 718 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ILE A 723 " --> pdb=" O   ARG A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 766
      removed outlier: 3.638A  pdb=" N   LEU A 761 " --> pdb=" O   TYR A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 821 through 823
      No H-bonds generated for 'chain 'A' and resid 821 through 823'
    Processing helix  chain 'A' and resid 842 through 851
      Proline residue:  A 847  - end of helix
    Processing helix  chain 'A' and resid 854 through 856
      No H-bonds generated for 'chain 'A' and resid 854 through 856'
    Processing helix  chain 'A' and resid 879 through 886
      removed outlier: 3.714A  pdb=" N   LYS A 885 " --> pdb=" O   SER A 881 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   PHE A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 905 through 914
    Processing helix  chain 'A' and resid 916 through 918
      No H-bonds generated for 'chain 'A' and resid 916 through 918'
    Processing helix  chain 'A' and resid 927 through 934
    Processing helix  chain 'A' and resid 943 through 948
    Processing helix  chain 'A' and resid 951 through 966
      removed outlier: 3.741A  pdb=" N   VAL A 957 " --> pdb=" O   SER A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 998
      removed outlier: 4.129A  pdb=" N   SER A 998 " --> pdb=" O   LEU A 994 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 150
      removed outlier: 3.807A  pdb=" N   ASN B 149 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 157
      No H-bonds generated for 'chain 'B' and resid 154 through 157'
    Processing helix  chain 'B' and resid 159 through 193
      removed outlier: 6.867A  pdb=" N   ILE B 168 " --> pdb=" O   ALA B 164 " (cutoff:3.500A)
      removed outlier: 8.829A  pdb=" N   VAL B 169 " --> pdb=" O   GLN B 165 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU B 170 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   VAL B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   THR B 182 " --> pdb=" O   SER B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 211
    Processing helix  chain 'B' and resid 213 through 249
      removed outlier: 3.606A  pdb=" N   GLY B 217 " --> pdb=" O   PRO B 213 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ALA B 232 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLY B 237 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU B 248 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 276
      removed outlier: 3.570A  pdb=" N   VAL B 265 " --> pdb=" O   ARG B 261 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   VAL B 266 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 303
      removed outlier: 3.800A  pdb=" N   LYS B 284 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ALA B 285 " --> pdb=" O   TRP B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 315
      removed outlier: 3.787A  pdb=" N   LYS B 315 " --> pdb=" O   ASP B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 325
      No H-bonds generated for 'chain 'B' and resid 322 through 325'
    Processing helix  chain 'B' and resid 340 through 350
      Proline residue:  B 349  - end of helix
    Processing helix  chain 'B' and resid 358 through 363
      removed outlier: 4.026A  pdb=" N   SER B 361 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   GLY B 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 394
      Proline residue:  B 372  - end of helix
      removed outlier: 3.620A  pdb=" N   MET B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   PHE B 380 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 422
      No H-bonds generated for 'chain 'B' and resid 420 through 422'
    Processing helix  chain 'B' and resid 428 through 433
    Processing helix  chain 'B' and resid 446 through 449
      No H-bonds generated for 'chain 'B' and resid 446 through 449'
    Processing helix  chain 'B' and resid 454 through 485
      removed outlier: 3.548A  pdb=" N   LEU B 466 " --> pdb=" O   GLY B 463 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   SER B 467 " --> pdb=" O   ALA B 464 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA B 469 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   CYS B 472 " --> pdb=" O   ALA B 469 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA B 476 " --> pdb=" O   LEU B 473 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   LYS B 478 " --> pdb=" O   SER B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 522
      removed outlier: 3.778A  pdb=" N   ILE B 522 " --> pdb=" O   ALA B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 532
      No H-bonds generated for 'chain 'B' and resid 529 through 532'
    Processing helix  chain 'B' and resid 535 through 552
      removed outlier: 3.802A  pdb=" N   SER B 539 " --> pdb=" O   PHE B 535 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS B 547 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE B 548 " --> pdb=" O   ASN B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 584
      removed outlier: 3.537A  pdb=" N   ALA B 574 " --> pdb=" O   ALA B 570 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER B 577 " --> pdb=" O   GLY B 573 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL B 578 " --> pdb=" O   ALA B 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 604
      removed outlier: 3.501A  pdb=" N   VAL B 596 " --> pdb=" O   ALA B 592 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B 599 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL B 603 " --> pdb=" O   LEU B 599 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE B 604 " --> pdb=" O   LEU B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 632
      removed outlier: 3.541A  pdb=" N   GLY B 630 " --> pdb=" O   SER B 626 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ASN B 632 " --> pdb=" O   SER B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 640
      No H-bonds generated for 'chain 'B' and resid 638 through 640'
    Processing helix  chain 'B' and resid 656 through 665
      removed outlier: 3.965A  pdb=" N   PHE B 665 " --> pdb=" O   PHE B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 702
      removed outlier: 3.800A  pdb=" N   THR B 697 " --> pdb=" O   ALA B 693 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 717 through 727
    Processing helix  chain 'B' and resid 751 through 766
      removed outlier: 3.678A  pdb=" N   LEU B 761 " --> pdb=" O   TYR B 757 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 821 through 823
      No H-bonds generated for 'chain 'B' and resid 821 through 823'
    Processing helix  chain 'B' and resid 846 through 852
    Processing helix  chain 'B' and resid 869 through 885
      removed outlier: 3.673A  pdb=" N   MET B 872 " --> pdb=" O   ILE B 869 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ASP B 873 " --> pdb=" O   ASN B 870 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN B 874 " --> pdb=" O   ARG B 871 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LYS B 877 " --> pdb=" O   GLN B 874 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU B 883 " --> pdb=" O   ILE B 880 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 905 through 914
    Processing helix  chain 'B' and resid 927 through 934
      removed outlier: 3.931A  pdb=" N   ASN B 931 " --> pdb=" O   GLU B 927 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   GLU B 932 " --> pdb=" O   ALA B 928 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   MET B 933 " --> pdb=" O   THR B 929 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 943 through 947
    Processing helix  chain 'B' and resid 950 through 966
      removed outlier: 3.547A  pdb=" N   GLN B 956 " --> pdb=" O   LYS B 952 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL B 957 " --> pdb=" O   SER B 953 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 987 through 996
    Processing helix  chain 'C' and resid 165 through 169
    Processing sheet with id=  A, first strand: chain 'A' and resid 672 through 675
      removed outlier: 6.802A  pdb=" N   CYS A 645 " --> pdb=" O   ILE A 673 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   GLY A 675 " --> pdb=" O   CYS A 645 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL A 647 " --> pdb=" O   GLY A 675 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE A 737 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   LEU A 648 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   VAL A 739 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   GLY A 770 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   VAL A 740 " --> pdb=" O   GLY A 770 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   CYS A 772 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ILE A 973 " --> pdb=" O   ILE A1006 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   ILE A1008 " --> pdb=" O   ILE A 973 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   ILE A 975 " --> pdb=" O   ILE A1008 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU A 972 " --> pdb=" O   THR A 830 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   THR A 976 " --> pdb=" O   TYR A 834 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LYS A 860 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   ILE A 833 " --> pdb=" O   LYS A 860 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ARG A 862 " --> pdb=" O   ILE A 833 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 677 through 679
      removed outlier: 6.846A  pdb=" N   VAL A 712 " --> pdb=" O   LEU A 678 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  B
    Processing sheet with id=  C, first strand: chain 'B' and resid 892 through 896
      removed outlier: 3.539A  pdb=" N   VAL B 863 " --> pdb=" O   GLU B 892 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU B 972 " --> pdb=" O   ASP B 832 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   TYR B 834 " --> pdb=" O   LEU B 972 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL B 974 " --> pdb=" O   TYR B 834 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   ILE B 975 " --> pdb=" O   PRO B1004 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ILE B1006 " --> pdb=" O   ILE B 975 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   GLY B 741 " --> pdb=" O   LEU B 648 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   PHE B 708 " --> pdb=" O   CYS B 674 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   HIS B 676 " --> pdb=" O   PHE B 708 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   SER B 710 " --> pdb=" O   HIS B 676 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   LEU B 678 " --> pdb=" O   SER B 710 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL B 712 " --> pdb=" O   LEU B 678 " (cutoff:3.500A)

    558 hydrogen bonds defined for protein.
    1560 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.07

  Time building geometry restraints manager: 5.82 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2261
        1.32 -     1.45: 3756
        1.45 -     1.57: 7794
        1.57 -     1.69: 16
        1.69 -     1.82: 121
  Bond restraints: 13948
  Sorted by residual:
  bond pdb=" C4  ATP B1101 "
       pdb=" C5  ATP B1101 "
    ideal  model  delta    sigma   weight residual
    1.388  1.456 -0.068 1.00e-02 1.00e+04 4.68e+01
  bond pdb=" C4  ATP A1101 "
       pdb=" C5  ATP A1101 "
    ideal  model  delta    sigma   weight residual
    1.388  1.453 -0.065 1.00e-02 1.00e+04 4.28e+01
  bond pdb=" C5  ATP A1101 "
       pdb=" C6  ATP A1101 "
    ideal  model  delta    sigma   weight residual
    1.409  1.470 -0.061 1.00e-02 1.00e+04 3.70e+01
  bond pdb=" C5  ATP B1101 "
       pdb=" C6  ATP B1101 "
    ideal  model  delta    sigma   weight residual
    1.409  1.467 -0.058 1.00e-02 1.00e+04 3.33e+01
  bond pdb=" C5  ATP A1101 "
       pdb=" N7  ATP A1101 "
    ideal  model  delta    sigma   weight residual
    1.387  1.338  0.049 1.00e-02 1.00e+04 2.43e+01
  ... (remaining 13943 not shown)

  Histogram of bond angle deviations from ideal:
       97.15 -   105.03: 270
      105.03 -   112.91: 7504
      112.91 -   120.78: 6868
      120.78 -   128.66: 4200
      128.66 -   136.54: 132
  Bond angle restraints: 18974
  Sorted by residual:
  angle pdb=" PB  ATP B1101 "
        pdb=" O3B ATP B1101 "
        pdb=" PG  ATP B1101 "
      ideal   model   delta    sigma   weight residual
     139.87  118.04   21.83 1.00e+00 1.00e+00 4.77e+02
  angle pdb=" PB  ATP A1101 "
        pdb=" O3B ATP A1101 "
        pdb=" PG  ATP A1101 "
      ideal   model   delta    sigma   weight residual
     139.87  118.43   21.44 1.00e+00 1.00e+00 4.60e+02
  angle pdb=" PA  ATP A1101 "
        pdb=" O3A ATP A1101 "
        pdb=" PB  ATP A1101 "
      ideal   model   delta    sigma   weight residual
     136.83  116.66   20.17 1.00e+00 1.00e+00 4.07e+02
  angle pdb=" PA  ATP B1101 "
        pdb=" O3A ATP B1101 "
        pdb=" PB  ATP B1101 "
      ideal   model   delta    sigma   weight residual
     136.83  117.78   19.05 1.00e+00 1.00e+00 3.63e+02
  angle pdb=" N   SER A 319 "
        pdb=" CA  SER A 319 "
        pdb=" C   SER A 319 "
      ideal   model   delta    sigma   weight residual
     111.07  121.59  -10.52 1.07e+00 8.73e-01 9.67e+01
  ... (remaining 18969 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 7372
       17.97 -    35.95: 640
       35.95 -    53.92: 149
       53.92 -    71.89: 38
       71.89 -    89.86: 15
  Dihedral angle restraints: 8214
    sinusoidal: 3268
      harmonic: 4946
  Sorted by residual:
  dihedral pdb=" CB  CYS B 416 "
           pdb=" SG  CYS B 416 "
           pdb=" SG  CYS B 421 "
           pdb=" CB  CYS B 421 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.59   81.41     1      1.00e+01 1.00e-02 8.17e+01
  dihedral pdb=" CA  ASN A 258 "
           pdb=" C   ASN A 258 "
           pdb=" N   ASP A 259 "
           pdb=" CA  ASP A 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.26   26.74     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  CYS A 436 "
           pdb=" C   CYS A 436 "
           pdb=" N   HIS A 437 "
           pdb=" CA  HIS A 437 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.45  -25.55     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 8211 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1933
       0.084 -    0.169: 189
       0.169 -    0.253: 20
       0.253 -    0.337: 9
       0.337 -    0.421: 1
  Chirality restraints: 2152
  Sorted by residual:
  chirality pdb=" CA  ARG B 685 "
            pdb=" N   ARG B 685 "
            pdb=" C   ARG B 685 "
            pdb=" CB  ARG B 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.44e+00
  chirality pdb=" CA  TYR B 499 "
            pdb=" N   TYR B 499 "
            pdb=" C   TYR B 499 "
            pdb=" CB  TYR B 499 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CA  PHE B 494 "
            pdb=" N   PHE B 494 "
            pdb=" C   PHE B 494 "
            pdb=" CB  PHE B 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.54e+00
  ... (remaining 2149 not shown)

  Planarity restraints: 2353
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 678 "    0.014 2.00e-02 2.50e+03   2.92e-02 8.51e+00
        pdb=" C   LEU B 678 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LEU B 678 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ILE B 679 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 255 "   -0.040 5.00e-02 4.00e+02   6.23e-02 6.21e+00
        pdb=" N   PRO A 256 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 256 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 256 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 902 "    0.038 5.00e-02 4.00e+02   5.92e-02 5.60e+00
        pdb=" N   PRO A 903 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO A 903 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 903 "    0.035 5.00e-02 4.00e+02
  ... (remaining 2350 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1546
        2.74 -     3.28: 13159
        3.28 -     3.82: 21443
        3.82 -     4.36: 26228
        4.36 -     4.90: 45767
  Nonbonded interactions: 108143
  Sorted by model distance:
  nonbonded pdb=" O   HIS B 750 "
            pdb=" OG1 THR B 753 "
     model   vdw
     2.199 2.440
  nonbonded pdb=" NH2 ARG B 703 "
            pdb=" O   ALA B 818 "
     model   vdw
     2.220 2.520
  nonbonded pdb=" OH  TYR B 156 "
            pdb=" OG  SER B 296 "
     model   vdw
     2.229 2.440
  nonbonded pdb=" O   PRO B 530 "
            pdb=" ND2 ASN B 534 "
     model   vdw
     2.230 2.520
  nonbonded pdb=" OD2 ASP B 839 "
            pdb=" OG1 THR B 843 "
     model   vdw
     2.230 2.440
  ... (remaining 108138 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 131 through 605 or resid 620 through 1018 or resid 1101 th \ 
rough 1102))
  selection = (chain 'B' and (resid 131 through 865 or resid 878 through 1018 or resid 1101 th \ 
rough 1102))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          7.440
  Check model and map are aligned:         0.220
  Set scattering table:                    0.140
  Process input model:                     38.090
  Find NCS groups from input model:        0.850
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.068  13948  Z= 0.565
  Angle     :  0.988  21.835  18974  Z= 0.628
  Chirality :  0.058   0.421   2152
  Planarity :  0.006   0.062   2353
  Dihedral  : 15.099  89.865   5030
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  1.65 %
    Favored  : 96.14 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.19), residues: 1706
  helix: -0.63 (0.17), residues: 918
  sheet: -0.65 (0.50), residues: 111
  loop : -1.97 (0.21), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 993 
 HIS   0.004   0.001   HIS B 234 
 PHE   0.030   0.002   PHE B 654 
 TYR   0.025   0.002   TYR A 443 
 ARG   0.011   0.001   ARG B 854 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 179
  time to evaluate  : 1.615 
Fit side-chains
REVERT: A  256 PRO cc_start: 0.7493 (Cg_exo) cc_final: 0.7259 (Cg_endo)
REVERT: A  821 ILE cc_start: 0.8730 (mm) cc_final: 0.8479 (mp)
REVERT: A  912 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7823 (mm-30)
  outliers start: 32
  outliers final: 4
  residues processed: 204
  average time/residue: 1.3957
  time to fit residues: 309.8631
Evaluate side-chains
  139 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 135
  time to evaluate  : 1.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  682 HIS
Chi-restraints excluded: chain B residue  685 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 133 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   chunk 154 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
A 258 ASN
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 747 GLN
A 956 GLN
A1014 ASN
B 149 ASN
B 406 ASN
B 481 GLN
B 502 ASN
B 644 GLN
B 696 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13948  Z= 0.183
  Angle     :  0.550   7.726  18974  Z= 0.285
  Chirality :  0.042   0.172   2152
  Planarity :  0.004   0.056   2353
  Dihedral  :  8.998  88.191   1953
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  9.72 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.20), residues: 1706
  helix:  0.20 (0.17), residues: 920
  sheet: -0.63 (0.47), residues: 124
  loop : -1.79 (0.21), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 586 
 HIS   0.006   0.001   HIS B 234 
 PHE   0.011   0.001   PHE A 665 
 TYR   0.010   0.001   TYR A 499 
 ARG   0.005   0.000   ARG B 685 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 1.487 
Fit side-chains
REVERT: A  912 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7619 (mm-30)
REVERT: B  635 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7562 (pm20)
REVERT: B  686 MET cc_start: 0.5228 (OUTLIER) cc_final: 0.4900 (mpt)
REVERT: B  692 ILE cc_start: 0.7898 (mm) cc_final: 0.7613 (pt)
  outliers start: 30
  outliers final: 10
  residues processed: 174
  average time/residue: 1.2459
  time to fit residues: 238.4507
Evaluate side-chains
  145 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 1.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  994 LEU
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  635 GLU
Chi-restraints excluded: chain B residue  685 ARG
Chi-restraints excluded: chain B residue  686 MET
Chi-restraints excluded: chain B residue 1001 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 128 optimal weight:    2.9990
   chunk 105 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   chunk 154 optimal weight:    2.9990
   chunk 167 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   chunk 153 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 684 GLN
A 900 ASN
B 359 ASN
B 502 ASN
B 781 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  13948  Z= 0.253
  Angle     :  0.545   7.433  18974  Z= 0.278
  Chirality :  0.042   0.175   2152
  Planarity :  0.004   0.039   2353
  Dihedral  :  8.476  86.131   1949
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.20 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.20), residues: 1706
  helix:  0.48 (0.18), residues: 923
  sheet: -0.49 (0.46), residues: 125
  loop : -1.69 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 138 
 HIS   0.002   0.001   HIS A 682 
 PHE   0.012   0.001   PHE B 661 
 TYR   0.010   0.001   TYR A 443 
 ARG   0.006   0.000   ARG B 777 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 135
  time to evaluate  : 1.978 
Fit side-chains
REVERT: A  912 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7523 (mm-30)
  outliers start: 38
  outliers final: 17
  residues processed: 158
  average time/residue: 1.3180
  time to fit residues: 229.1372
Evaluate side-chains
  150 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  820 THR
Chi-restraints excluded: chain A residue  994 LEU
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  672 MET
Chi-restraints excluded: chain B residue  685 ARG
Chi-restraints excluded: chain B residue  819 THR
Chi-restraints excluded: chain B residue  964 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 152 optimal weight:    4.9990
   chunk 116 optimal weight:    0.9990
   chunk 80 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0170
   chunk 73 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 155 optimal weight:    0.5980
   chunk 164 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 147 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.6820

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 ASN
B 502 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13948  Z= 0.147
  Angle     :  0.480   5.810  18974  Z= 0.246
  Chirality :  0.039   0.138   2152
  Planarity :  0.003   0.038   2353
  Dihedral  :  7.785  87.938   1949
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.58 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.20), residues: 1706
  helix:  0.80 (0.18), residues: 923
  sheet: -0.20 (0.46), residues: 125
  loop : -1.60 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 138 
 HIS   0.001   0.000   HIS A 676 
 PHE   0.017   0.001   PHE A 918 
 TYR   0.009   0.001   TYR A 990 
 ARG   0.006   0.000   ARG B 777 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 148
  time to evaluate  : 1.553 
Fit side-chains
   revert: symmetry clash
REVERT: A  750 HIS cc_start: 0.8256 (t-90) cc_final: 0.7933 (t-90)
REVERT: A  768 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8455 (t0)
REVERT: A  821 ILE cc_start: 0.8734 (mm) cc_final: 0.8445 (mp)
REVERT: A  912 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7491 (mm-30)
REVERT: A  966 TYR cc_start: 0.6546 (m-80) cc_final: 0.6333 (m-80)
REVERT: B  321 ARG cc_start: 0.6981 (mtt90) cc_final: 0.6778 (mtt90)
  outliers start: 33
  outliers final: 13
  residues processed: 170
  average time/residue: 1.2229
  time to fit residues: 231.0054
Evaluate side-chains
  149 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  768 ASN
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  566 ASN
Chi-restraints excluded: chain B residue  685 ARG
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  964 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 136 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0020
   chunk 122 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 140 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   chunk 147 optimal weight:    9.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    1.7394

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 502 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13948  Z= 0.254
  Angle     :  0.522   6.172  18974  Z= 0.265
  Chirality :  0.042   0.173   2152
  Planarity :  0.004   0.039   2353
  Dihedral  :  7.741  87.743   1949
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 13.92 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.20), residues: 1706
  helix:  0.76 (0.18), residues: 928
  sheet: -0.15 (0.46), residues: 125
  loop : -1.59 (0.22), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 138 
 HIS   0.003   0.000   HIS A 682 
 PHE   0.011   0.001   PHE B 223 
 TYR   0.011   0.001   TYR A 990 
 ARG   0.006   0.000   ARG B 777 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 134
  time to evaluate  : 1.507 
Fit side-chains
REVERT: A  294 MET cc_start: 0.8460 (mmp) cc_final: 0.8236 (mmt)
REVERT: A  768 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8461 (t0)
REVERT: A  821 ILE cc_start: 0.8735 (mm) cc_final: 0.8426 (mp)
REVERT: A  912 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7591 (mm-30)
REVERT: A  966 TYR cc_start: 0.6734 (m-80) cc_final: 0.6483 (m-80)
REVERT: B  321 ARG cc_start: 0.7080 (mtt90) cc_final: 0.6799 (mtt90)
REVERT: B  935 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6926 (mtm180)
REVERT: B  944 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7637 (tm-30)
  outliers start: 42
  outliers final: 21
  residues processed: 166
  average time/residue: 1.1640
  time to fit residues: 213.1521
Evaluate side-chains
  154 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  768 ASN
Chi-restraints excluded: chain A residue  816 GLU
Chi-restraints excluded: chain A residue  957 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  566 ASN
Chi-restraints excluded: chain B residue  672 MET
Chi-restraints excluded: chain B residue  685 ARG
Chi-restraints excluded: chain B residue  819 THR
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  964 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 55 optimal weight:    0.0010
   chunk 147 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 96 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 164 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 ASN
B 502 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13948  Z= 0.155
  Angle     :  0.488   7.787  18974  Z= 0.247
  Chirality :  0.040   0.175   2152
  Planarity :  0.003   0.038   2353
  Dihedral  :  7.427  88.840   1949
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.23 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.82 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.21), residues: 1706
  helix:  0.92 (0.18), residues: 927
  sheet: -0.07 (0.45), residues: 131
  loop : -1.53 (0.22), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 138 
 HIS   0.001   0.000   HIS A 682 
 PHE   0.010   0.001   PHE B 661 
 TYR   0.009   0.001   TYR A 990 
 ARG   0.004   0.000   ARG B 777 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 137
  time to evaluate  : 1.624 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 MET cc_start: 0.8443 (mmp) cc_final: 0.8210 (mmt)
REVERT: A  821 ILE cc_start: 0.8711 (mm) cc_final: 0.8412 (mp)
REVERT: A  912 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7514 (mm-30)
REVERT: A  966 TYR cc_start: 0.6534 (m-80) cc_final: 0.6259 (m-80)
REVERT: B  321 ARG cc_start: 0.7005 (mtt90) cc_final: 0.6722 (mtt90)
REVERT: B  635 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7534 (mp0)
REVERT: B  935 ARG cc_start: 0.7222 (mtp180) cc_final: 0.6853 (mtp180)
REVERT: B  944 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7630 (tm-30)
  outliers start: 37
  outliers final: 18
  residues processed: 163
  average time/residue: 1.2029
  time to fit residues: 215.8583
Evaluate side-chains
  150 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  635 GLU
Chi-restraints excluded: chain B residue  685 ARG
Chi-restraints excluded: chain B residue  819 THR
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  959 LEU
Chi-restraints excluded: chain B residue  964 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 158 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 138 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 163 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 ASN
B 502 ASN
B 868 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  13948  Z= 0.394
  Angle     :  0.602   7.229  18974  Z= 0.303
  Chirality :  0.045   0.168   2152
  Planarity :  0.004   0.042   2353
  Dihedral  :  7.852  86.527   1949
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.09 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.20), residues: 1706
  helix:  0.60 (0.18), residues: 929
  sheet: -0.18 (0.46), residues: 125
  loop : -1.59 (0.22), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 993 
 HIS   0.004   0.001   HIS A 682 
 PHE   0.017   0.002   PHE A 918 
 TYR   0.011   0.001   TYR B 513 
 ARG   0.004   0.000   ARG B 777 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 123
  time to evaluate  : 1.551 
Fit side-chains
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6756 (mm-30)
REVERT: A  692 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7702 (mp)
REVERT: A  774 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7417 (ttt)
REVERT: A  912 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7561 (mm-30)
REVERT: B  566 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7623 (t0)
REVERT: B  635 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7520 (mp0)
REVERT: B  944 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7747 (tm-30)
  outliers start: 46
  outliers final: 25
  residues processed: 156
  average time/residue: 1.2231
  time to fit residues: 210.2543
Evaluate side-chains
  152 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 1.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  692 ILE
Chi-restraints excluded: chain A residue  733 MET
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  774 MET
Chi-restraints excluded: chain A residue  816 GLU
Chi-restraints excluded: chain A residue  820 THR
Chi-restraints excluded: chain A residue  957 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  566 ASN
Chi-restraints excluded: chain B residue  635 GLU
Chi-restraints excluded: chain B residue  685 ARG
Chi-restraints excluded: chain B residue  819 THR
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  964 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 104 optimal weight:    0.7980
   chunk 111 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9980
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 ASN
B 406 ASN
B 502 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13948  Z= 0.165
  Angle     :  0.495   7.951  18974  Z= 0.252
  Chirality :  0.040   0.186   2152
  Planarity :  0.003   0.039   2353
  Dihedral  :  7.393  87.984   1949
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.54 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.20), residues: 1706
  helix:  0.87 (0.18), residues: 927
  sheet: -0.15 (0.44), residues: 134
  loop : -1.54 (0.22), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 138 
 HIS   0.001   0.000   HIS A 234 
 PHE   0.013   0.001   PHE A 911 
 TYR   0.008   0.001   TYR A 990 
 ARG   0.005   0.000   ARG B 777 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 1.839 
Fit side-chains
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6816 (mm-30)
REVERT: A  912 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7473 (mm-30)
REVERT: B  147 MET cc_start: 0.8593 (mtt) cc_final: 0.8254 (mtt)
REVERT: B  935 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6801 (mtm180)
REVERT: B  944 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7718 (tm-30)
  outliers start: 30
  outliers final: 16
  residues processed: 155
  average time/residue: 1.2356
  time to fit residues: 211.3099
Evaluate side-chains
  146 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  816 GLU
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  685 ARG
Chi-restraints excluded: chain B residue  819 THR
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  964 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 156 optimal weight:    3.9990
   chunk 143 optimal weight:    2.9990
   chunk 152 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 119 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 137 optimal weight:    0.5980
   chunk 144 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 161 optimal weight:    0.0060
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 ASN
B 502 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13948  Z= 0.140
  Angle     :  0.474   7.269  18974  Z= 0.241
  Chirality :  0.040   0.178   2152
  Planarity :  0.003   0.038   2353
  Dihedral  :  7.071  89.923   1945
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.23 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.21), residues: 1706
  helix:  1.07 (0.18), residues: 927
  sheet:  0.11 (0.44), residues: 134
  loop : -1.43 (0.23), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 138 
 HIS   0.001   0.000   HIS B 894 
 PHE   0.015   0.001   PHE A 911 
 TYR   0.008   0.001   TYR A 990 
 ARG   0.006   0.000   ARG B 321 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 1.460 
Fit side-chains
   revert: symmetry clash
REVERT: A  912 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7516 (mm-30)
REVERT: A  990 TYR cc_start: 0.7689 (t80) cc_final: 0.7025 (t80)
REVERT: B  147 MET cc_start: 0.8596 (mtt) cc_final: 0.8339 (mtt)
REVERT: B  531 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7963 (mt)
REVERT: B  935 ARG cc_start: 0.7218 (mtp180) cc_final: 0.6812 (mtm180)
REVERT: B  944 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7724 (tm-30)
  outliers start: 22
  outliers final: 14
  residues processed: 152
  average time/residue: 1.2110
  time to fit residues: 202.4783
Evaluate side-chains
  147 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 1.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  685 ARG
Chi-restraints excluded: chain B residue  819 THR
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  964 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 76 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 169 optimal weight:    5.9990
   chunk 155 optimal weight:    0.3980
   chunk 134 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 104 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 143 optimal weight:    0.0770
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 ASN
B 406 ASN
B 502 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13948  Z= 0.144
  Angle     :  0.477  11.504  18974  Z= 0.241
  Chirality :  0.039   0.174   2152
  Planarity :  0.003   0.038   2353
  Dihedral  :  6.930  89.674   1945
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 18.26 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.21), residues: 1706
  helix:  1.15 (0.18), residues: 928
  sheet:  0.22 (0.44), residues: 134
  loop : -1.35 (0.23), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 138 
 HIS   0.001   0.000   HIS A 437 
 PHE   0.015   0.001   PHE A 911 
 TYR   0.007   0.001   TYR A 990 
 ARG   0.006   0.000   ARG B 321 

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

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

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3412 Ramachandran restraints generated.
    1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 1.513 
Fit side-chains
   revert: symmetry clash
REVERT: A  854 ARG cc_start: 0.7889 (pmt170) cc_final: 0.5922 (mtp85)
REVERT: A  912 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7541 (mm-30)
REVERT: A  990 TYR cc_start: 0.7664 (t80) cc_final: 0.6979 (t80)
REVERT: B  178 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8058 (m)
REVERT: B  531 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7917 (mt)
REVERT: B  935 ARG cc_start: 0.7210 (mtp180) cc_final: 0.6802 (mtm180)
REVERT: B  944 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7730 (tm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 149
  average time/residue: 1.2112
  time to fit residues: 198.7352
Evaluate side-chains
  148 residues out of total 1452 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  685 ARG
Chi-restraints excluded: chain B residue  819 THR
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain C residue  147 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 124 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0980
   chunk 37 optimal weight:    0.3980
   chunk 135 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 138 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 118 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 ASN
B 502 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.168610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.123141 restraints weight = 15937.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.31
r_work: 0.3445 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13948  Z= 0.176
  Angle     :  0.488  10.368  18974  Z= 0.246
  Chirality :  0.040   0.171   2152
  Planarity :  0.003   0.039   2353
  Dihedral  :  6.961  89.411   1945
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.99 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.21), residues: 1706
  helix:  1.10 (0.18), residues: 935
  sheet:  0.29 (0.44), residues: 134
  loop : -1.32 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 138 
 HIS   0.002   0.000   HIS A 682 
 PHE   0.016   0.001   PHE A 911 
 TYR   0.008   0.001   TYR A 990 
 ARG   0.005   0.000   ARG B 321 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4677.74 seconds
wall clock time: 84 minutes 12.12 seconds (5052.12 seconds total)