Starting phenix.real_space_refine
on Tue Feb 20 04:58:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmo_18498/02_2024/8qmo_18498_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmo_18498/02_2024/8qmo_18498.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmo_18498/02_2024/8qmo_18498_trim_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmo_18498/02_2024/8qmo_18498_trim_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmo_18498/02_2024/8qmo_18498_trim_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmo_18498/02_2024/8qmo_18498.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmo_18498/02_2024/8qmo_18498.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmo_18498/02_2024/8qmo_18498_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmo_18498/02_2024/8qmo_18498_trim_updated.pdb"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 8
    Type Number    sf(0)   Gaussians
     Mo      2     10.26       5
     P       4      5.49       5
     Mg      2      5.21       5
     S      68      5.16       5
     C    8901      2.51       5
     N    2380      2.21       5
     O    2695      1.98       5
     H   12884      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP   52": "OD1" <-> "OD2"
    Residue "A TYR  373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  424": "OE1" <-> "OE2"
    Residue "A GLU  561": "OE1" <-> "OE2"
    Residue "B GLU  141": "OE1" <-> "OE2"
    Residue "B GLU  200": "OE1" <-> "OE2"
    Residue "B GLU  281": "OE1" <-> "OE2"
    Residue "B GLU  303": "OE1" <-> "OE2"
    Residue "B TYR  373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU  443": "OE1" <-> "OE2"
    Residue "B GLU  471": "OE1" <-> "OE2"
    Residue "B GLU  527": "OE1" <-> "OE2"
    Residue "B GLU  643": "OE1" <-> "OE2"
    Residue "D GLU  345": "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: 26936
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 10152
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 624, 10143
          Classifications: {'peptide': 624}
          Link IDs: {'PTRANS': 17, 'TRANS': 606}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 624, 10143
          Classifications: {'peptide': 624}
          Link IDs: {'PTRANS': 17, 'TRANS': 606}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 10216
    Chain: "B"
      Number of atoms: 10357
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 637, 10333
          Classifications: {'peptide': 637}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 619}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 637, 10333
          Classifications: {'peptide': 637}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 619}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 10391
    Chain: "C"
      Number of atoms: 4914
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 304, 4875
          Classifications: {'peptide': 304}
          Link IDs: {'PTRANS': 14, 'TRANS': 289}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 304, 4875
          Classifications: {'peptide': 304}
          Link IDs: {'PTRANS': 14, 'TRANS': 289}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4881
    Chain: "D"
      Number of atoms: 1407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1407
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 9, 'TRANS': 146}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'MOO': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'MOO': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 40
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 20
          Unusual residues: {'W62': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 20
          Unusual residues: {'W62': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG B 612 " occ=0.47
      ... (46 atoms not shown)
      pdb="HH22BARG B 612 " occ=0.53
    residue:
      pdb=" N  ASER C 256 " occ=0.34
      ... (20 atoms not shown)
      pdb=" HG BSER C 256 " occ=0.66
    residue:
      pdb=" C1 AW62 D 501 " occ=0.50
      ... (38 atoms not shown)
      pdb=" C9 BW62 D 501 " occ=0.50
  Time building chain proxies: 19.90, per 1000 atoms: 0.74
  Number of scatterers: 26936
  At special positions: 0
  Unit cell: (133.6, 118.57, 146.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Mo      2     41.97
     S      68     16.00
     P       4     15.00
     Mg      2     11.99
     O    2695      8.00
     N    2380      7.00
     C    8901      6.00
     H   12884      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM26857  O3A ADP A 802 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 19.22
  Conformation dependent library (CDL) restraints added in 4.8 seconds
  

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3288

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      71 helices and 10 sheets defined
      41.6% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 4.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 31
    Processing helix  chain 'A' and resid 36 through 59
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 95 through 103
    Processing helix  chain 'A' and resid 109 through 116
    Processing helix  chain 'A' and resid 132 through 138
    Processing helix  chain 'A' and resid 190 through 193
    Processing helix  chain 'A' and resid 195 through 205
    Processing helix  chain 'A' and resid 288 through 290
      No H-bonds generated for 'chain 'A' and resid 288 through 290'
    Processing helix  chain 'A' and resid 293 through 295
      No H-bonds generated for 'chain 'A' and resid 293 through 295'
    Processing helix  chain 'A' and resid 298 through 309
    Processing helix  chain 'A' and resid 372 through 374
      No H-bonds generated for 'chain 'A' and resid 372 through 374'
    Processing helix  chain 'A' and resid 398 through 421
      removed outlier: 4.005A  pdb=" N   ILE A 404 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG A 405 " --> pdb=" O   LYS A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 443
      removed outlier: 6.337A  pdb=" N   LYS A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   ASN A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A 437 " --> pdb=" O   PHE A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 454
      removed outlier: 3.635A  pdb=" N   GLU A 453 " --> pdb=" O   ARG A 449 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU A 454 " --> pdb=" O   ARG A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 474
    Processing helix  chain 'A' and resid 491 through 495
    Processing helix  chain 'A' and resid 501 through 505
    Processing helix  chain 'A' and resid 516 through 522
    Processing helix  chain 'A' and resid 547 through 570
      removed outlier: 5.145A  pdb=" N   ASN A 562 " --> pdb=" O   ALA A 558 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   LEU A 563 " --> pdb=" O   LYS A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 606
    Processing helix  chain 'A' and resid 617 through 619
      No H-bonds generated for 'chain 'A' and resid 617 through 619'
    Processing helix  chain 'A' and resid 633 through 644
    Processing helix  chain 'A' and resid 649 through 665
    Processing helix  chain 'A' and resid 673 through 688
    Processing helix  chain 'B' and resid 21 through 30
    Processing helix  chain 'B' and resid 36 through 60
    Processing helix  chain 'B' and resid 62 through 64
      No H-bonds generated for 'chain 'B' and resid 62 through 64'
    Processing helix  chain 'B' and resid 95 through 103
    Processing helix  chain 'B' and resid 109 through 116
    Processing helix  chain 'B' and resid 132 through 138
    Processing helix  chain 'B' and resid 190 through 193
    Processing helix  chain 'B' and resid 195 through 205
    Processing helix  chain 'B' and resid 288 through 290
      No H-bonds generated for 'chain 'B' and resid 288 through 290'
    Processing helix  chain 'B' and resid 293 through 295
      No H-bonds generated for 'chain 'B' and resid 293 through 295'
    Processing helix  chain 'B' and resid 298 through 309
    Processing helix  chain 'B' and resid 372 through 374
      No H-bonds generated for 'chain 'B' and resid 372 through 374'
    Processing helix  chain 'B' and resid 398 through 421
      removed outlier: 3.615A  pdb=" N   ILE B 404 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 443
      removed outlier: 6.458A  pdb=" N   LYS B 435 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ASN B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B 437 " --> pdb=" O   PHE B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 454
      removed outlier: 3.584A  pdb=" N   GLU B 453 " --> pdb=" O   ARG B 449 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU B 454 " --> pdb=" O   ARG B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 474
    Processing helix  chain 'B' and resid 491 through 495
    Processing helix  chain 'B' and resid 501 through 505
    Processing helix  chain 'B' and resid 516 through 522
      removed outlier: 3.927A  pdb=" N   TYR B 520 " --> pdb=" O   PRO B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 559
    Processing helix  chain 'B' and resid 561 through 570
    Processing helix  chain 'B' and resid 600 through 608
      removed outlier: 3.580A  pdb=" N   ALA B 608 " --> pdb=" O   ARG B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 614 through 619
      removed outlier: 3.505A  pdb=" N   MET B 617 " --> pdb=" O   ASN B 614 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   GLY B 618 " --> pdb=" O   SER B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 644
    Processing helix  chain 'B' and resid 649 through 665
    Processing helix  chain 'B' and resid 673 through 688
    Processing helix  chain 'B' and resid 716 through 720
    Processing helix  chain 'C' and resid 4 through 11
    Processing helix  chain 'C' and resid 72 through 79
      removed outlier: 3.607A  pdb=" N   THR C  79 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 95
      No H-bonds generated for 'chain 'C' and resid 92 through 95'
    Processing helix  chain 'C' and resid 98 through 100
      No H-bonds generated for 'chain 'C' and resid 98 through 100'
    Processing helix  chain 'C' and resid 140 through 142
      No H-bonds generated for 'chain 'C' and resid 140 through 142'
    Processing helix  chain 'C' and resid 167 through 169
      No H-bonds generated for 'chain 'C' and resid 167 through 169'
    Processing helix  chain 'C' and resid 172 through 192
      removed outlier: 3.875A  pdb=" N   LYS C 177 " --> pdb=" O   GLU C 173 " (cutoff:3.500A)
      Proline residue:  C 180  - end of helix
    Processing helix  chain 'C' and resid 196 through 215
      removed outlier: 3.698A  pdb=" N   MET C 214 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LYS C 215 " --> pdb=" O   ASN C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 244
      removed outlier: 3.742A  pdb=" N   GLN C 229 " --> pdb=" O   GLN C 225 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE C 230 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   THR C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
      Proline residue:  C 232  - end of helix
    Processing helix  chain 'C' and resid 247 through 260
      removed outlier: 3.803A  pdb=" N   LYS C 260 " --> pdb=" O  ASER C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 265 through 277
    Processing helix  chain 'C' and resid 281 through 294
    Processing helix  chain 'C' and resid 300 through 323
    Processing helix  chain 'D' and resid 302 through 307
    Processing helix  chain 'D' and resid 312 through 317
      removed outlier: 3.607A  pdb=" N   THR D 317 " --> pdb=" O   ALA D 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 322 through 324
      No H-bonds generated for 'chain 'D' and resid 322 through 324'
    Processing helix  chain 'D' and resid 327 through 343
      removed outlier: 4.738A  pdb=" N   LEU D 331 " --> pdb=" O   ALA D 328 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR D 343 " --> pdb=" O   MET D 340 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 396
    Processing helix  chain 'D' and resid 422 through 424
      No H-bonds generated for 'chain 'D' and resid 422 through 424'
    Processing sheet with id=  A, first strand: chain 'A' and resid 166 through 169
      removed outlier: 6.858A  pdb=" N   HIS A 184 " --> pdb=" O   GLU A 141 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   VAL A 143 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   VAL A 145 " --> pdb=" O   LYS A 180 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LYS A 180 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   THR A 147 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   GLY A 178 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ILE A  75 " --> pdb=" O   PRO A 212 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   THR A 214 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   TYR A 216 " --> pdb=" O   PRO A  77 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 360 through 364
      removed outlier: 6.975A  pdb=" N   LEU A 355 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   ASP A 364 " --> pdb=" O   ILE A 353 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   ILE A 353 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   LYS A 354 " --> pdb=" O   ILE A 377 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLY A 379 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   TYR A 356 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   VAL A 381 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A 317 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 533 through 535
      removed outlier: 6.065A  pdb=" N   ILE A 483 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 578 through 580
      removed outlier: 8.697A  pdb=" N   THR A 579 " --> pdb=" O   LYS A 624 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   LEU A 626 " --> pdb=" O   THR A 579 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 212 through 216
      removed outlier: 3.708A  pdb=" N   LYS B 142 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 317 through 323
      removed outlier: 3.743A  pdb=" N   ALA B 317 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS B 354 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   MET B 363 " --> pdb=" O   LEU B 355 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   VAL B 357 " --> pdb=" O   PHE B 361 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   PHE B 361 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 533 through 535
      removed outlier: 5.975A  pdb=" N   ILE B 483 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 577 through 580
      removed outlier: 3.836A  pdb=" N   LYS B 577 " --> pdb=" O   LYS B 624 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'C' and resid 15 through 19
      removed outlier: 3.618A  pdb=" N   ARG C  16 " --> pdb=" O   GLN C  87 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLN C  87 " --> pdb=" O   ARG C  16 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE C  18 " --> pdb=" O   ILE C  85 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   ILE C  85 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU C 148 " --> pdb=" O   CYS C  90 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   THR C  35 " --> pdb=" O   LEU C 155 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   VAL C 157 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LYS C  33 " --> pdb=" O   VAL C 157 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'D' and resid 287 through 291
      removed outlier: 6.817A  pdb=" N   LEU D 370 " --> pdb=" O   ASP D 377 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ILE D 379 " --> pdb=" O   ARG D 368 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ARG D 368 " --> pdb=" O   ILE D 379 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   VAL D 381 " --> pdb=" O   ASN D 366 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ASN D 366 " --> pdb=" O   VAL D 381 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   GLN D 383 " --> pdb=" O   GLN D 364 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   GLN D 364 " --> pdb=" O   GLN D 383 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   TRP D 362 " --> pdb=" O   PRO D 385 " (cutoff:3.500A)

    554 hydrogen bonds defined for protein.
    1310 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: 10.85

  Time building geometry restraints manager: 20.08 seconds

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

  Histogram of bond lengths:
        0.80 -     1.00: 12602
        1.00 -     1.21: 284
        1.21 -     1.41: 5737
        1.41 -     1.61: 8452
        1.61 -     1.82: 122
  Bond restraints: 27197
  Sorted by residual:
  bond pdb=" N   SER B 206 "
       pdb=" H   SER B 206 "
    ideal  model  delta    sigma   weight residual
    0.860  1.038 -0.178 2.00e-02 2.50e+03 7.89e+01
  bond pdb=" N   GLU C 318 "
       pdb=" H   GLU C 318 "
    ideal  model  delta    sigma   weight residual
    0.860  1.037 -0.177 2.00e-02 2.50e+03 7.83e+01
  bond pdb=" N   VAL A 403 "
       pdb=" H   VAL A 403 "
    ideal  model  delta    sigma   weight residual
    0.860  1.037 -0.177 2.00e-02 2.50e+03 7.82e+01
  bond pdb=" N   ALA C 322 "
       pdb=" H   ALA C 322 "
    ideal  model  delta    sigma   weight residual
    0.860  1.036 -0.176 2.00e-02 2.50e+03 7.79e+01
  bond pdb=" N   ASP B 278 "
       pdb=" H   ASP B 278 "
    ideal  model  delta    sigma   weight residual
    0.860  1.036 -0.176 2.00e-02 2.50e+03 7.78e+01
  ... (remaining 27192 not shown)

  Histogram of bond angle deviations from ideal:
       79.25 -    90.66: 8
       90.66 -   102.07: 46
      102.07 -   113.47: 32273
      113.47 -   124.88: 15512
      124.88 -   136.29: 910
  Bond angle restraints: 48749
  Sorted by residual:
  angle pdb="HD12 ILE A 288 "
        pdb=" CD1 ILE A 288 "
        pdb="HD13 ILE A 288 "
      ideal   model   delta    sigma   weight residual
     110.00   79.81   30.19 3.00e+00 1.11e-01 1.01e+02
  angle pdb=" HZ1 LYS C 103 "
        pdb=" NZ  LYS C 103 "
        pdb=" HZ2 LYS C 103 "
      ideal   model   delta    sigma   weight residual
     109.00   79.25   29.75 3.00e+00 1.11e-01 9.83e+01
  angle pdb=" HZ2 LYS C 103 "
        pdb=" NZ  LYS C 103 "
        pdb=" HZ3 LYS C 103 "
      ideal   model   delta    sigma   weight residual
     109.00   79.38   29.62 3.00e+00 1.11e-01 9.75e+01
  angle pdb=" CG1 ILE A 288 "
        pdb=" CD1 ILE A 288 "
        pdb="HD13 ILE A 288 "
      ideal   model   delta    sigma   weight residual
     109.00   80.00   29.00 3.00e+00 1.11e-01 9.34e+01
  angle pdb="HD11 ILE A 288 "
        pdb=" CD1 ILE A 288 "
        pdb="HD12 ILE A 288 "
      ideal   model   delta    sigma   weight residual
     110.00   81.07   28.93 3.00e+00 1.11e-01 9.30e+01
  ... (remaining 48744 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 11205
       17.85 -    35.69: 1071
       35.69 -    53.54: 395
       53.54 -    71.38: 104
       71.38 -    89.23: 29
  Dihedral angle restraints: 12804
    sinusoidal: 7008
      harmonic: 5796
  Sorted by residual:
  dihedral pdb=" CA  LYS C  66 "
           pdb=" C   LYS C  66 "
           pdb=" N   LYS C  67 "
           pdb=" CA  LYS C  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.40   22.60     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  GLU B  20 "
           pdb=" C   GLU B  20 "
           pdb=" N   ILE B  21 "
           pdb=" CA  ILE B  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.46  -19.54     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  GLY C  65 "
           pdb=" C   GLY C  65 "
           pdb=" N   LYS C  66 "
           pdb=" CA  LYS C  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.49   19.51     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 12801 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1716
       0.045 -    0.090: 278
       0.090 -    0.135: 116
       0.135 -    0.180: 7
       0.180 -    0.225: 8
  Chirality restraints: 2125
  Sorted by residual:
  chirality pdb=" CA  VAL A 403 "
            pdb=" N   VAL A 403 "
            pdb=" C   VAL A 403 "
            pdb=" CB  VAL A 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE A 400 "
            pdb=" N   ILE A 400 "
            pdb=" C   ILE A 400 "
            pdb=" CB  ILE A 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  GLN B 279 "
            pdb=" N   GLN B 279 "
            pdb=" C   GLN B 279 "
            pdb=" CB  GLN B 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 2122 not shown)

  Planarity restraints: 4002
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 283 "   -0.171 2.00e-02 2.50e+03   4.78e-01 3.43e+03
        pdb=" CG  ASN B 283 "    0.013 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 283 "    0.173 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 283 "    0.000 2.00e-02 2.50e+03
        pdb="HD21 ASN B 283 "   -0.817 2.00e-02 2.50e+03
        pdb="HD22 ASN B 283 "    0.803 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 397 "   -0.337 2.00e-02 2.50e+03   4.28e-01 2.75e+03
        pdb=" CD  GLN A 397 "    0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 397 "    0.328 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 397 "   -0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN A 397 "   -0.670 2.00e-02 2.50e+03
        pdb="HE22 GLN A 397 "    0.657 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 207 "    0.344 2.00e-02 2.50e+03   4.06e-01 2.47e+03
        pdb=" CD  GLN B 207 "   -0.028 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 207 "   -0.329 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 207 "   -0.003 2.00e-02 2.50e+03
        pdb="HE21 GLN B 207 "   -0.608 2.00e-02 2.50e+03
        pdb="HE22 GLN B 207 "    0.626 2.00e-02 2.50e+03
  ... (remaining 3999 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 406
        2.08 -     2.71: 42471
        2.71 -     3.34: 75948
        3.34 -     3.97: 97519
        3.97 -     4.60: 152377
  Nonbonded interactions: 368721
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 424 "
            pdb=" H   GLU A 424 "
     model   vdw
     1.449 1.850
  nonbonded pdb=" OE1 GLU A 492 "
            pdb=" H   GLU A 492 "
     model   vdw
     1.518 1.850
  nonbonded pdb="HH22 ARG B 506 "
            pdb=" O   PRO B 544 "
     model   vdw
     1.607 1.850
  nonbonded pdb=" H   TYR C  38 "
            pdb=" OG  SER C  53 "
     model   vdw
     1.618 1.850
  nonbonded pdb=" HG  SER A 124 "
            pdb=" OE1 GLU A 384 "
     model   vdw
     1.631 1.850
  ... (remaining 368716 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 11 through 34 or resid 36 through 319 or (resid 320 and (n \ 
ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ 
D2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name  \ 
HD1 or name HD2 or name HE1)) or resid 321 through 457 or (resid 458 and (name N \ 
 or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or \ 
 name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 o \ 
r name HE1 or name HE2)) or resid 459 through 611 or resid 613 through 690 or re \ 
sid 801 through 803))
  selection = (chain 'B' and (resid 11 through 34 or resid 36 through 219 or resid 276 through \ 
 611 or resid 613 through 690 or resid 801 through 803))
}

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=0.32 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:             1.610
  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:             0.420
  Extract box with map and model:          11.120
  Check model and map are aligned:         0.360
  Set scattering table:                    0.220
  Process input model:                     94.460
  Find NCS groups from input model:        1.310
  Set up NCS constraints:                  0.140
  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:13.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  122.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14312  Z= 0.235
  Angle     :  0.628  10.264  19297  Z= 0.352
  Chirality :  0.042   0.225   2125
  Planarity :  0.003   0.059   2467
  Dihedral  : 18.259  89.227   5497
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.93 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 24.61 %
    Favored  : 73.31 %
  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:  0.67 (0.21), residues: 1715
  helix:  1.74 (0.20), residues: 730
  sheet:  0.38 (0.31), residues: 278
  loop : -0.91 (0.23), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 157 
 HIS   0.004   0.001   HIS B 625 
 PHE   0.011   0.001   PHE C 324 
 TYR   0.010   0.001   TYR B 596 
 ARG   0.004   0.000   ARG B 338 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 2.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  389 GLU cc_start: 0.7660 (mp0) cc_final: 0.7364 (mp0)
  outliers start: 29
  outliers final: 20
  residues processed: 178
  average time/residue: 2.9805
  time to fit residues: 578.8203
Evaluate side-chains
  162 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 2.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  586 SER
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain C residue  220 SER
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  339 ARG
Chi-restraints excluded: chain D residue  383 GLN
Chi-restraints excluded: chain D residue  406 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    3.9990
   chunk 128 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 133 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 154 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
B  23 GLN
B  80 GLN
B 100 ASN
B 283 ASN
B 625 HIS
C 229 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.0551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14312  Z= 0.178
  Angle     :  0.532   6.485  19297  Z= 0.277
  Chirality :  0.039   0.146   2125
  Planarity :  0.004   0.057   2467
  Dihedral  :  6.686  68.852   1941
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.52 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 24.48 %
    Favored  : 73.12 %
  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:  0.52 (0.21), residues: 1715
  helix:  1.46 (0.20), residues: 719
  sheet:  0.55 (0.31), residues: 280
  loop : -0.88 (0.23), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 157 
 HIS   0.006   0.001   HIS B 625 
 PHE   0.012   0.001   PHE A 329 
 TYR   0.010   0.001   TYR A 134 
 ARG   0.006   0.000   ARG C 191 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 2.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  153 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6512 (tm-30)
REVERT: B  443 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7583 (tp30)
REVERT: B  465 GLU cc_start: 0.7450 (pp20) cc_final: 0.7247 (pp20)
REVERT: C  261 TYR cc_start: 0.5713 (m-10) cc_final: 0.4926 (m-80)
REVERT: C  263 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5865 (p0)
REVERT: C  321 LYS cc_start: 0.7528 (mtmm) cc_final: 0.6862 (mttp)
REVERT: D  389 GLU cc_start: 0.7641 (mp0) cc_final: 0.7391 (mp0)
  outliers start: 34
  outliers final: 12
  residues processed: 173
  average time/residue: 2.9029
  time to fit residues: 549.8882
Evaluate side-chains
  154 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 2.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain B residue   25 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  153 GLU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  443 GLU
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain D residue  388 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 128 optimal weight:    0.8980
   chunk 105 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 154 optimal weight:    1.9990
   chunk 167 optimal weight:    5.9990
   chunk 137 optimal weight:    0.9990
   chunk 153 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
B  80 GLN
B 283 ASN
B 625 HIS
B 674 GLN
C 229 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14312  Z= 0.208
  Angle     :  0.533   6.628  19297  Z= 0.276
  Chirality :  0.040   0.144   2125
  Planarity :  0.004   0.054   2467
  Dihedral  :  5.789  76.004   1914
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.05 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 24.16 %
    Favored  : 73.44 %
  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:  0.27 (0.21), residues: 1715
  helix:  1.13 (0.20), residues: 731
  sheet:  0.50 (0.31), residues: 278
  loop : -0.94 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 157 
 HIS   0.004   0.001   HIS B 625 
 PHE   0.012   0.001   PHE A 334 
 TYR   0.012   0.001   TYR B 596 
 ARG   0.006   0.000   ARG C 304 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 2.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.7504 (t0) cc_final: 0.7176 (t0)
REVERT: B  153 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6544 (tm-30)
REVERT: B  443 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7631 (tp30)
REVERT: B  465 GLU cc_start: 0.7498 (pp20) cc_final: 0.7254 (pp20)
REVERT: C  261 TYR cc_start: 0.5802 (m-10) cc_final: 0.5036 (m-80)
REVERT: D  329 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8162 (m-30)
REVERT: D  389 GLU cc_start: 0.7644 (mp0) cc_final: 0.7395 (mp0)
REVERT: D  401 LYS cc_start: 0.5976 (mtmm) cc_final: 0.5567 (mtpm)
  outliers start: 34
  outliers final: 14
  residues processed: 173
  average time/residue: 2.7530
  time to fit residues: 522.1258
Evaluate side-chains
  155 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 2.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain B residue   25 MET
Chi-restraints excluded: chain B residue  153 GLU
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  443 GLU
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  329 ASP
Chi-restraints excluded: chain D residue  388 ASP
Chi-restraints excluded: chain D residue  406 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 152 optimal weight:    3.9990
   chunk 116 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 155 optimal weight:    4.9990
   chunk 164 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 147 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
B  80 GLN
** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 383 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.0959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14312  Z= 0.252
  Angle     :  0.547   6.787  19297  Z= 0.283
  Chirality :  0.040   0.144   2125
  Planarity :  0.004   0.055   2467
  Dihedral  :  5.734  82.863   1909
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 24.03 %
    Favored  : 73.57 %
  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:  0.15 (0.21), residues: 1715
  helix:  1.04 (0.20), residues: 730
  sheet:  0.42 (0.30), residues: 278
  loop : -0.99 (0.23), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 157 
 HIS   0.004   0.001   HIS B 320 
 PHE   0.015   0.001   PHE A 334 
 TYR   0.013   0.002   TYR B 596 
 ARG   0.003   0.000   ARG C 191 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 146
  time to evaluate  : 2.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7268 (mtm-85)
REVERT: B  153 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6555 (tm-30)
REVERT: B  443 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7663 (tp30)
REVERT: B  465 GLU cc_start: 0.7574 (pp20) cc_final: 0.7309 (pp20)
REVERT: C  261 TYR cc_start: 0.5781 (m-10) cc_final: 0.4761 (m-80)
REVERT: C  263 ASP cc_start: 0.6086 (OUTLIER) cc_final: 0.5796 (p0)
REVERT: D  279 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6867 (mt-10)
REVERT: D  389 GLU cc_start: 0.7650 (mp0) cc_final: 0.7402 (mp0)
REVERT: D  401 LYS cc_start: 0.5996 (mtmm) cc_final: 0.5580 (mtpm)
  outliers start: 34
  outliers final: 15
  residues processed: 168
  average time/residue: 2.8662
  time to fit residues: 527.2725
Evaluate side-chains
  160 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 2.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain B residue   25 MET
Chi-restraints excluded: chain B residue   82 ARG
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  153 GLU
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  443 GLU
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain D residue  279 GLU
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  406 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 136 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 122 optimal weight:    0.0870
   chunk 67 optimal weight:    4.9990
   chunk 140 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 147 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.2164

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

Flipped N/Q/H residues before XYZ refinement:
A 397 GLN
B  23 GLN
B  80 GLN
** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 229 GLN
D 383 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14312  Z= 0.221
  Angle     :  0.532   6.635  19297  Z= 0.276
  Chirality :  0.040   0.145   2125
  Planarity :  0.004   0.052   2467
  Dihedral  :  5.731  85.700   1909
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.51 %
    Favored  : 73.83 %
  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:  0.13 (0.21), residues: 1715
  helix:  0.99 (0.20), residues: 731
  sheet:  0.42 (0.30), residues: 278
  loop : -0.97 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 157 
 HIS   0.003   0.001   HIS B 625 
 PHE   0.013   0.001   PHE A 334 
 TYR   0.012   0.001   TYR B 596 
 ARG   0.003   0.000   ARG C 191 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 145
  time to evaluate  : 2.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  153 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6558 (tm-30)
REVERT: B  443 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7618 (tp30)
REVERT: C   60 MET cc_start: 0.2803 (OUTLIER) cc_final: 0.2084 (ttt)
REVERT: C  261 TYR cc_start: 0.5758 (m-10) cc_final: 0.4924 (m-80)
REVERT: C  290 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.5981 (tppp)
REVERT: D  279 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6850 (mt-10)
REVERT: D  389 GLU cc_start: 0.7635 (mp0) cc_final: 0.7417 (mp0)
REVERT: D  401 LYS cc_start: 0.5968 (mtmm) cc_final: 0.5556 (mtpm)
  outliers start: 38
  outliers final: 15
  residues processed: 170
  average time/residue: 2.8347
  time to fit residues: 527.9224
Evaluate side-chains
  163 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 2.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain B residue   25 MET
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  153 GLU
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  443 GLU
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  290 LYS
Chi-restraints excluded: chain D residue  279 GLU
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  406 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 147 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 164 optimal weight:    0.6980
   chunk 136 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  80 GLN
** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 229 GLN
D 383 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
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   0.039  14312  Z= 0.209
  Angle     :  0.526   6.651  19297  Z= 0.272
  Chirality :  0.039   0.145   2125
  Planarity :  0.004   0.046   2467
  Dihedral  :  5.708  85.682   1909
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 23.90 %
    Favored  : 73.77 %
  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:  0.18 (0.21), residues: 1715
  helix:  1.05 (0.20), residues: 721
  sheet:  0.37 (0.30), residues: 285
  loop : -0.91 (0.23), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 157 
 HIS   0.007   0.001   HIS C  94 
 PHE   0.013   0.001   PHE A 334 
 TYR   0.011   0.001   TYR B 596 
 ARG   0.002   0.000   ARG C 191 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 147
  time to evaluate  : 2.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 MET cc_start: 0.7884 (mmt) cc_final: 0.7672 (mmt)
REVERT: B  153 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6591 (tm-30)
REVERT: B  195 GLU cc_start: 0.7507 (tt0) cc_final: 0.7226 (tt0)
REVERT: B  443 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7633 (tp30)
REVERT: C   60 MET cc_start: 0.2814 (OUTLIER) cc_final: 0.2084 (ttt)
REVERT: C  261 TYR cc_start: 0.5768 (m-10) cc_final: 0.4910 (m-80)
REVERT: C  290 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.5989 (tppp)
REVERT: D  279 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6846 (mt-10)
REVERT: D  389 GLU cc_start: 0.7632 (mp0) cc_final: 0.7411 (mp0)
REVERT: D  401 LYS cc_start: 0.5962 (mtmm) cc_final: 0.5551 (mtpm)
  outliers start: 33
  outliers final: 16
  residues processed: 171
  average time/residue: 2.8349
  time to fit residues: 536.1874
Evaluate side-chains
  162 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 2.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain B residue  153 GLU
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  443 GLU
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  290 LYS
Chi-restraints excluded: chain D residue  279 GLU
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  388 ASP
Chi-restraints excluded: chain D residue  406 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 158 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 120 optimal weight:    2.9990
   chunk 138 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 163 optimal weight:    0.5980
   chunk 102 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  23 GLN
B  80 GLN
B 674 GLN
C 229 GLN
D 383 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14312  Z= 0.176
  Angle     :  0.508   6.543  19297  Z= 0.262
  Chirality :  0.039   0.144   2125
  Planarity :  0.004   0.049   2467
  Dihedral  :  5.568  81.914   1909
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 23.70 %
    Favored  : 73.96 %
  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: 1715
  helix:  1.08 (0.20), residues: 728
  sheet:  0.43 (0.30), residues: 285
  loop : -0.91 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 157 
 HIS   0.003   0.001   HIS B 625 
 PHE   0.011   0.001   PHE A 334 
 TYR   0.010   0.001   TYR B 426 
 ARG   0.002   0.000   ARG C 304 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 2.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  561 GLU cc_start: 0.7585 (tp30) cc_final: 0.7125 (tp30)
REVERT: B  153 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6637 (tm-30)
REVERT: B  443 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7611 (tp30)
REVERT: C   60 MET cc_start: 0.2659 (OUTLIER) cc_final: 0.1960 (ttt)
REVERT: C  261 TYR cc_start: 0.5786 (m-10) cc_final: 0.4922 (m-80)
REVERT: C  290 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.5999 (tppp)
REVERT: D  279 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6854 (mt-10)
REVERT: D  389 GLU cc_start: 0.7619 (mp0) cc_final: 0.7399 (mp0)
REVERT: D  401 LYS cc_start: 0.5949 (mtmm) cc_final: 0.5544 (mtpm)
  outliers start: 33
  outliers final: 14
  residues processed: 169
  average time/residue: 2.7824
  time to fit residues: 515.3014
Evaluate side-chains
  161 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 2.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain B residue  153 GLU
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  443 GLU
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  290 LYS
Chi-restraints excluded: chain D residue  279 GLU
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  406 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 128 optimal weight:    9.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B  23 GLN
B  80 GLN
C 229 GLN
D 383 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14312  Z= 0.188
  Angle     :  0.514   6.554  19297  Z= 0.264
  Chirality :  0.039   0.144   2125
  Planarity :  0.004   0.048   2467
  Dihedral  :  5.557  82.594   1907
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 23.77 %
    Favored  : 74.03 %
  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: 1715
  helix:  1.08 (0.20), residues: 728
  sheet:  0.43 (0.30), residues: 285
  loop : -0.92 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 157 
 HIS   0.003   0.001   HIS B 625 
 PHE   0.012   0.001   PHE A 334 
 TYR   0.010   0.001   TYR B 426 
 ARG   0.002   0.000   ARG C 304 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 2.155 
Fit side-chains
   revert: symmetry clash
REVERT: B  153 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6694 (tm-30)
REVERT: B  443 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7625 (tp30)
REVERT: C   60 MET cc_start: 0.2577 (OUTLIER) cc_final: 0.1878 (ttt)
REVERT: C  261 TYR cc_start: 0.5799 (m-10) cc_final: 0.4895 (m-80)
REVERT: C  290 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.5999 (tppp)
REVERT: D  279 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6846 (mt-10)
REVERT: D  389 GLU cc_start: 0.7623 (mp0) cc_final: 0.7402 (mp0)
REVERT: D  401 LYS cc_start: 0.5950 (mtmm) cc_final: 0.5544 (mtpm)
  outliers start: 31
  outliers final: 17
  residues processed: 163
  average time/residue: 2.7771
  time to fit residues: 496.3284
Evaluate side-chains
  165 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 2.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  153 GLU
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  443 GLU
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  290 LYS
Chi-restraints excluded: chain D residue  279 GLU
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  388 ASP
Chi-restraints excluded: chain D residue  406 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 156 optimal weight:    0.3980
   chunk 143 optimal weight:    2.9990
   chunk 152 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 137 optimal weight:    0.7980
   chunk 144 optimal weight:    0.6980
   chunk 100 optimal weight:    0.0980
   chunk 161 optimal weight:    5.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  80 GLN
** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 229 GLN
D 383 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14312  Z= 0.153
  Angle     :  0.496   6.324  19297  Z= 0.254
  Chirality :  0.038   0.142   2125
  Planarity :  0.004   0.047   2467
  Dihedral  :  5.390  78.033   1907
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 24.22 %
    Favored  : 74.09 %
  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:  0.31 (0.21), residues: 1715
  helix:  1.15 (0.21), residues: 728
  sheet:  0.48 (0.31), residues: 285
  loop : -0.87 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 157 
 HIS   0.003   0.001   HIS B 625 
 PHE   0.010   0.001   PHE A 334 
 TYR   0.010   0.001   TYR B 426 
 ARG   0.002   0.000   ARG C 304 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 2.456 
Fit side-chains
   revert: symmetry clash
REVERT: B  195 GLU cc_start: 0.7516 (tt0) cc_final: 0.7231 (tt0)
REVERT: B  443 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7595 (tp30)
REVERT: C   60 MET cc_start: 0.2573 (OUTLIER) cc_final: 0.1866 (ttt)
REVERT: C  261 TYR cc_start: 0.5797 (m-10) cc_final: 0.4896 (m-80)
REVERT: D  389 GLU cc_start: 0.7612 (mp0) cc_final: 0.7387 (mp0)
REVERT: D  401 LYS cc_start: 0.5943 (mtmm) cc_final: 0.5543 (mtpm)
  outliers start: 23
  outliers final: 12
  residues processed: 160
  average time/residue: 2.7864
  time to fit residues: 490.7073
Evaluate side-chains
  158 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 2.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  443 GLU
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain D residue  388 ASP
Chi-restraints excluded: chain D residue  406 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   chunk 169 optimal weight:    4.9990
   chunk 155 optimal weight:    9.9990
   chunk 134 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 107 optimal weight:    0.5980
   chunk 143 optimal weight:    0.7980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
B  23 GLN
B  80 GLN
B 351 ASN
C 229 GLN
D 383 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  14312  Z= 0.234
  Angle     :  0.536   6.896  19297  Z= 0.277
  Chirality :  0.040   0.143   2125
  Planarity :  0.004   0.049   2467
  Dihedral  :  5.620  86.241   1906
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 24.61 %
    Favored  : 73.90 %
  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:  0.20 (0.21), residues: 1715
  helix:  1.04 (0.20), residues: 730
  sheet:  0.38 (0.30), residues: 290
  loop : -0.91 (0.23), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 157 
 HIS   0.004   0.001   HIS B 625 
 PHE   0.014   0.001   PHE A 334 
 TYR   0.013   0.002   TYR B 596 
 ARG   0.005   0.000   ARG C 304 

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 2.451 
Fit side-chains
   revert: symmetry clash
REVERT: B  195 GLU cc_start: 0.7543 (tt0) cc_final: 0.7244 (tt0)
REVERT: B  443 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7581 (tp30)
REVERT: C   60 MET cc_start: 0.2760 (OUTLIER) cc_final: 0.2052 (ttt)
REVERT: C  261 TYR cc_start: 0.5811 (m-10) cc_final: 0.4867 (m-80)
REVERT: D  389 GLU cc_start: 0.7650 (mp0) cc_final: 0.7421 (mp0)
REVERT: D  401 LYS cc_start: 0.5948 (mtmm) cc_final: 0.5542 (mtpm)
  outliers start: 20
  outliers final: 12
  residues processed: 160
  average time/residue: 2.7129
  time to fit residues: 477.1449
Evaluate side-chains
  157 residues out of total 1527 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 2.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  443 GLU
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  406 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 135 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 138 optimal weight:    0.0030
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 118 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
B  80 GLN
B 351 ASN
** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 194 HIS
C 229 GLN
D 383 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.145718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.109245 restraints weight = 82125.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 3.88
r_work: 0.3018 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3009
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14312  Z= 0.151
  Angle     :  0.497   6.193  19297  Z= 0.254
  Chirality :  0.038   0.143   2125
  Planarity :  0.004   0.048   2467
  Dihedral  :  5.354  78.331   1906
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 24.81 %
    Favored  : 73.83 %
  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:  0.34 (0.21), residues: 1715
  helix:  1.16 (0.21), residues: 728
  sheet:  0.43 (0.30), residues: 290
  loop : -0.82 (0.24), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 157 
 HIS   0.003   0.001   HIS B 625 
 PHE   0.010   0.001   PHE A 334 
 TYR   0.010   0.001   TYR B 426 
 ARG   0.004   0.000   ARG C 304 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9443.77 seconds
wall clock time: 167 minutes 4.06 seconds (10024.06 seconds total)