Starting phenix.real_space_refine
on Fri Jan 19 07:58:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/01_2024/7r87_24310.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/01_2024/7r87_24310.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/01_2024/7r87_24310.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/01_2024/7r87_24310.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/01_2024/7r87_24310.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/01_2024/7r87_24310.pdb"
  }
  resolution = 3.4
  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: 4
    Type Number    sf(0)   Gaussians
     S      67      5.16       5
     C    6966      2.51       5
     N    1827      2.21       5
     O    1933      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   77": "OE1" <-> "OE2"
    Residue "A GLU  169": "OE1" <-> "OE2"
    Residue "A GLU  237": "OE1" <-> "OE2"
    Residue "A GLU  279": "OE1" <-> "OE2"
    Residue "A GLU  452": "OE1" <-> "OE2"
    Residue "A TYR  458": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  257": "NH1" <-> "NH2"
    Residue "B ARG  339": "NH1" <-> "NH2"
    Residue "B GLU  474": "OE1" <-> "OE2"
    Residue "B GLU  503": "OE1" <-> "OE2"
    Residue "B TYR  516": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  571": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG   38": "NH1" <-> "NH2"
    Residue "C GLU   54": "OE1" <-> "OE2"
    Residue "C ARG   63": "NH1" <-> "NH2"
    Residue "C GLU   73": "OE1" <-> "OE2"
    Residue "C ARG  108": "NH1" <-> "NH2"
    Residue "C GLU  110": "OE1" <-> "OE2"
    Residue "D GLU  101": "OE1" <-> "OE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib"
  Total number of atoms: 10793
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 586, 4608
          Classifications: {'peptide': 586}
          Link IDs: {'PTRANS': 21, 'TRANS': 564}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 564, 4481
          Classifications: {'peptide': 564}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 539}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 901
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "D"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 803
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100}
  Time building chain proxies: 6.19, per 1000 atoms: 0.57
  Number of scatterers: 10793
  At special positions: 0
  Unit cell: (113.288, 104.958, 126.616, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      67     16.00
     O    1933      8.00
     N    1827      7.00
     C    6966      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 587 " - pdb=" SG  CYS A 600 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  41 " - pdb=" SG  CYS C 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  43 " - pdb=" SG  CYS D 108 " distance=2.03

  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: 4.19
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2536

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      53.4% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 101
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 160 through 175
      removed outlier: 4.390A  pdb=" N   PHE A 164 " --> pdb=" O   ASN A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 181
      removed outlier: 3.504A  pdb=" N   VAL A 180 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA A 181 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 177 through 181'
    Processing helix  chain 'A' and resid 194 through 208
    Processing helix  chain 'A' and resid 224 through 241
    Processing helix  chain 'A' and resid 276 through 287
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 311 through 331
      removed outlier: 3.583A  pdb=" N   GLU A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE A 316 " --> pdb=" O   LYS A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 347
      removed outlier: 3.916A  pdb=" N   HIS A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 381
    Processing helix  chain 'A' and resid 382 through 402
      removed outlier: 3.571A  pdb=" N   VAL A 386 " --> pdb=" O   ASN A 382 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   ASN A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LEU A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 454
      Proline residue:  A 431  - end of helix
      Proline residue:  A 443  - end of helix
      removed outlier: 4.134A  pdb=" N   GLN A 454 " --> pdb=" O   ASP A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 491
      Proline residue:  A 473  - end of helix
      removed outlier: 4.567A  pdb=" N   TRP A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   THR A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 524
      Proline residue:  A 509  - end of helix
    Processing helix  chain 'A' and resid 526 through 545
    Processing helix  chain 'A' and resid 551 through 555
    Processing helix  chain 'A' and resid 556 through 564
      removed outlier: 3.562A  pdb=" N   TYR A 564 " --> pdb=" O   LYS A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 580
      removed outlier: 4.277A  pdb=" N   TYR A 570 " --> pdb=" O   THR A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 613
      removed outlier: 4.157A  pdb=" N   PHE A 608 " --> pdb=" O   GLN A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 617
      removed outlier: 4.239A  pdb=" N   THR A 617 " --> pdb=" O   PRO A 614 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 614 through 617'
    Processing helix  chain 'A' and resid 619 through 649
      removed outlier: 4.577A  pdb=" N   ILE A 631 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      Proline residue:  A 632  - end of helix
      removed outlier: 4.572A  pdb=" N   HIS A 647 " --> pdb=" O   LYS A 643 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 120
      removed outlier: 3.556A  pdb=" N   VAL B 117 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 147
    Processing helix  chain 'B' and resid 162 through 175
    Processing helix  chain 'B' and resid 180 through 195
    Processing helix  chain 'B' and resid 214 through 227
    Processing helix  chain 'B' and resid 244 through 261
      removed outlier: 3.518A  pdb=" N   GLY B 261 " --> pdb=" O   ARG B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 279
      removed outlier: 3.639A  pdb=" N   LEU B 279 " --> pdb=" O   ASP B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 308
    Processing helix  chain 'B' and resid 316 through 325
      removed outlier: 3.925A  pdb=" N   THR B 325 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 353
      removed outlier: 3.615A  pdb=" N   GLU B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LYS B 341 " --> pdb=" O   ALA B 337 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU B 350 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 411
    Processing helix  chain 'B' and resid 413 through 435
    Processing helix  chain 'B' and resid 444 through 458
    Processing helix  chain 'B' and resid 458 through 473
      removed outlier: 4.333A  pdb=" N   ASN B 462 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 485
      removed outlier: 3.516A  pdb=" N   GLY B 485 " --> pdb=" O   GLU B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 490 through 513
      removed outlier: 4.628A  pdb=" N   PHE B 494 " --> pdb=" O   GLY B 490 " (cutoff:3.500A)
      Proline residue:  B 502  - end of helix
    Processing helix  chain 'B' and resid 514 through 516
      No H-bonds generated for 'chain 'B' and resid 514 through 516'
    Processing helix  chain 'B' and resid 525 through 553
    Processing helix  chain 'B' and resid 555 through 573
    Processing helix  chain 'B' and resid 585 through 593
      removed outlier: 3.685A  pdb=" N   TRP B 589 " --> pdb=" O   THR B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 608
      removed outlier: 3.511A  pdb=" N   TRP B 598 " --> pdb=" O   SER B 594 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 633
    Processing helix  chain 'B' and resid 634 through 638
      removed outlier: 3.592A  pdb=" N   SER B 637 " --> pdb=" O   GLU B 634 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   TYR B 638 " --> pdb=" O   LEU B 635 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 634 through 638'
    Processing helix  chain 'B' and resid 639 through 665
    Processing helix  chain 'C' and resid 72 through 76
    Processing helix  chain 'D' and resid 99 through 103
      removed outlier: 3.640A  pdb=" N   ASP D 102 " --> pdb=" O   GLU D  99 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU D 103 " --> pdb=" O   SER D 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 99 through 103'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72
      removed outlier: 5.936A  pdb=" N   LYS A  70 " --> pdb=" O   TYR A  45 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   TYR A  45 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 72
      removed outlier: 5.936A  pdb=" N   LYS A  70 " --> pdb=" O   TYR A  45 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   TYR A  45 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   ALA A  43 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LEU A 110 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132
      removed outlier: 3.522A  pdb=" N   THR A 248 " --> pdb=" O   PHE A 216 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE A  81 " --> pdb=" O   LYS A 262 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   ALA A 264 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   CYS A  83 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   LEU A 266 " --> pdb=" O   CYS A  83 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU A  85 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE A 263 " --> pdb=" O   CYS A 274 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   CYS A 274 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ILE A 265 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 96
      removed outlier: 7.445A  pdb=" N   PHE B  93 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   ARG B  50 " --> pdb=" O   PHE B  93 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   VAL B  95 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   GLU B  48 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.620A  pdb=" N   SER B 268 " --> pdb=" O   LEU B 236 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLY B 105 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   MET B 100 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   LEU B 284 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ALA B 102 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   MET B 286 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ILE B 104 " --> pdb=" O   MET B 286 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   TYR B 293 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   THR B 287 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26
    Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 81
      removed outlier: 5.537A  pdb=" N   TRP C  66 " --> pdb=" O   ARG C  57 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ARG C  57 " --> pdb=" O   TRP C  66 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA C  68 " --> pdb=" O   TRP C  55 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27
    Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32
      removed outlier: 6.736A  pdb=" N   LEU D  31 " --> pdb=" O   GLU D 125 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR D 107 " --> pdb=" O   LEU D  56 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ILE D  68 " --> pdb=" O   TRP D  55 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   GLN D  57 " --> pdb=" O   ARG D  66 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ARG D  66 " --> pdb=" O   GLN D  57 " (cutoff:3.500A)

    595 hydrogen bonds defined for protein.
    1731 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: 3.23

  Time building geometry restraints manager: 4.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3438
        1.34 -     1.46: 2397
        1.46 -     1.58: 5083
        1.58 -     1.69: 0
        1.69 -     1.81: 107
  Bond restraints: 11025
  Sorted by residual:
  bond pdb=" C   ILE B 459 "
       pdb=" N   PRO B 460 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.013 1.28e-02 6.10e+03 1.05e+00
  bond pdb=" CB  PRO B 514 "
       pdb=" CG  PRO B 514 "
    ideal  model  delta    sigma   weight residual
    1.492  1.535 -0.043 5.00e-02 4.00e+02 7.47e-01
  bond pdb=" C   PHE A 442 "
       pdb=" N   PRO A 443 "
    ideal  model  delta    sigma   weight residual
    1.334  1.347 -0.013 1.51e-02 4.39e+03 7.01e-01
  bond pdb=" CA  ILE B 459 "
       pdb=" C   ILE B 459 "
    ideal  model  delta    sigma   weight residual
    1.524  1.533 -0.008 1.05e-02 9.07e+03 6.53e-01
  bond pdb=" CA  PRO B 514 "
       pdb=" CB  PRO B 514 "
    ideal  model  delta    sigma   weight residual
    1.531  1.536 -0.005 6.20e-03 2.60e+04 5.94e-01
  ... (remaining 11020 not shown)

  Histogram of bond angle deviations from ideal:
      100.62 -   107.30: 327
      107.30 -   113.97: 6146
      113.97 -   120.64: 4710
      120.64 -   127.31: 3641
      127.31 -   133.98: 96
  Bond angle restraints: 14920
  Sorted by residual:
  angle pdb=" N   ILE A 416 "
        pdb=" CA  ILE A 416 "
        pdb=" C   ILE A 416 "
      ideal   model   delta    sigma   weight residual
     112.96  109.27    3.69 1.00e+00 1.00e+00 1.36e+01
  angle pdb=" N   ILE B 307 "
        pdb=" CA  ILE B 307 "
        pdb=" C   ILE B 307 "
      ideal   model   delta    sigma   weight residual
     113.07  108.80    4.27 1.36e+00 5.41e-01 9.88e+00
  angle pdb=" C   THR B 488 "
        pdb=" N   THR B 489 "
        pdb=" CA  THR B 489 "
      ideal   model   delta    sigma   weight residual
     122.08  126.15   -4.07 1.47e+00 4.63e-01 7.66e+00
  angle pdb=" C   MET B 513 "
        pdb=" N   PRO B 514 "
        pdb=" CA  PRO B 514 "
      ideal   model   delta    sigma   weight residual
     121.65  119.14    2.51 1.01e+00 9.80e-01 6.16e+00
  angle pdb=" C   ASN A 551 "
        pdb=" N   ILE A 552 "
        pdb=" CA  ILE A 552 "
      ideal   model   delta    sigma   weight residual
     120.62  124.60   -3.98 1.64e+00 3.72e-01 5.90e+00
  ... (remaining 14915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 6085
       17.58 -    35.16: 394
       35.16 -    52.73: 66
       52.73 -    70.31: 13
       70.31 -    87.89: 7
  Dihedral angle restraints: 6565
    sinusoidal: 2612
      harmonic: 3953
  Sorted by residual:
  dihedral pdb=" CB  GLU A 452 "
           pdb=" CG  GLU A 452 "
           pdb=" CD  GLU A 452 "
           pdb=" OE1 GLU A 452 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.10   85.10     1      3.00e+01 1.11e-03 9.76e+00
  dihedral pdb=" CA  ARG A 157 "
           pdb=" CB  ARG A 157 "
           pdb=" CG  ARG A 157 "
           pdb=" CD  ARG A 157 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.93  -58.07     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CA  GLN A 126 "
           pdb=" CB  GLN A 126 "
           pdb=" CG  GLN A 126 "
           pdb=" CD  GLN A 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  113.64  -53.64     3      1.50e+01 4.44e-03 9.22e+00
  ... (remaining 6562 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1143
       0.027 -    0.054: 342
       0.054 -    0.082: 118
       0.082 -    0.109: 73
       0.109 -    0.136: 22
  Chirality restraints: 1698
  Sorted by residual:
  chirality pdb=" CA  THR B 489 "
            pdb=" N   THR B 489 "
            pdb=" C   THR B 489 "
            pdb=" CB  THR B 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  THR A 430 "
            pdb=" N   THR A 430 "
            pdb=" C   THR A 430 "
            pdb=" CB  THR A 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  ILE C  90 "
            pdb=" N   ILE C  90 "
            pdb=" C   ILE C  90 "
            pdb=" CB  ILE C  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  ... (remaining 1695 not shown)

  Planarity restraints: 1879
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 555 "    0.017 5.00e-02 4.00e+02   2.53e-02 1.02e+00
        pdb=" N   PRO A 556 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 556 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 556 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 490 "    0.017 5.00e-02 4.00e+02   2.53e-02 1.02e+00
        pdb=" N   PRO B 491 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 491 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 491 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 276 "    0.016 5.00e-02 4.00e+02   2.50e-02 9.97e-01
        pdb=" N   PRO A 277 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1876 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 3492
        2.83 -     3.35: 9734
        3.35 -     3.87: 17750
        3.87 -     4.38: 19445
        4.38 -     4.90: 35334
  Nonbonded interactions: 85755
  Sorted by model distance:
  nonbonded pdb=" O   SER B 288 "
            pdb=" OG  SER B 288 "
     model   vdw
     2.317 2.440
  nonbonded pdb=" O   LYS B 605 "
            pdb=" OG  SER B 609 "
     model   vdw
     2.327 2.440
  nonbonded pdb=" O   ARG A 550 "
            pdb=" NH1 ARG A 550 "
     model   vdw
     2.343 2.520
  nonbonded pdb=" OE1 GLN A 417 "
            pdb=" ND2 ASN B 579 "
     model   vdw
     2.349 2.520
  nonbonded pdb=" OG  SER D  83 "
            pdb=" OG1 THR D  94 "
     model   vdw
     2.355 2.440
  ... (remaining 85750 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.530
  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:          5.810
  Check model and map are aligned:         0.170
  Set scattering table:                    0.100
  Process input model:                     32.080
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11025  Z= 0.104
  Angle     :  0.437   6.734  14920  Z= 0.252
  Chirality :  0.036   0.136   1698
  Planarity :  0.002   0.025   1879
  Dihedral  : 12.082  87.888   4020
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  5.33 %
    Favored  : 94.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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: -1.48 (0.21), residues: 1349
  helix:  0.27 (0.18), residues: 701
  sheet: -1.06 (0.36), residues: 181
  loop : -2.90 (0.24), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B 584 
 HIS   0.002   0.000   HIS A 470 
 PHE   0.006   0.000   PHE A 630 
 TYR   0.006   0.000   TYR B 472 
 ARG   0.001   0.000   ARG A 389 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 262
  time to evaluate  : 1.285 
Fit side-chains
REVERT: A  241 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.7244 (ttp-110)
REVERT: A  304 LEU cc_start: 0.8718 (tp) cc_final: 0.8440 (tp)
REVERT: B  160 ASN cc_start: 0.6780 (m-40) cc_final: 0.6426 (m-40)
REVERT: B  186 LYS cc_start: 0.7744 (tttp) cc_final: 0.7530 (tptm)
REVERT: B  220 ARG cc_start: 0.7348 (mtt-85) cc_final: 0.7084 (mtm-85)
REVERT: B  481 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7230 (mt-10)
REVERT: B  568 ASN cc_start: 0.8192 (m110) cc_final: 0.7986 (m-40)
REVERT: B  663 ARG cc_start: 0.7772 (ttt-90) cc_final: 0.7502 (ttt180)
  outliers start: 6
  outliers final: 4
  residues processed: 266
  average time/residue: 0.2786
  time to fit residues: 100.6589
Evaluate side-chains
  187 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 183
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  213 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0270
   chunk 64 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 122 optimal weight:   10.0000
   overall best weight:    1.5244

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

Flipped N/Q/H residues before XYZ refinement:
A  36 HIS
A 116 ASN
A 134 GLN
A 165 GLN
A 206 GLN
A 392 GLN
A 437 ASN
A 462 GLN
A 470 HIS
A 510 HIS
A 528 ASN
A 578 ASN
A 604 GLN
A 607 GLN
B  99 GLN
B 153 GLN
B 183 GLN
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 HIS
B 302 GLN
B 438 HIS
B 462 ASN
B 526 GLN
B 607 GLN
C  75 ASN
D  47 GLN
D  58 GLN
D  65 GLN

Total number of N/Q/H flips: 27

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11025  Z= 0.307
  Angle     :  0.626  10.011  14920  Z= 0.315
  Chirality :  0.043   0.242   1698
  Planarity :  0.004   0.056   1879
  Dihedral  :  4.050  55.378   1504
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 10.25 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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: -0.35 (0.22), residues: 1349
  helix:  1.12 (0.19), residues: 718
  sheet: -1.01 (0.34), residues: 190
  loop : -2.14 (0.27), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 128 
 HIS   0.008   0.001   HIS A 510 
 PHE   0.024   0.002   PHE B  93 
 TYR   0.019   0.002   TYR B 321 
 ARG   0.008   0.001   ARG A 389 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 1.313 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.6664 (mmt-90) cc_final: 0.6154 (mmp80)
REVERT: A  165 GLN cc_start: 0.7547 (tp-100) cc_final: 0.7093 (tp40)
REVERT: A  218 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8081 (mt-10)
REVERT: A  480 MET cc_start: 0.8369 (tpp) cc_final: 0.8122 (mmm)
REVERT: A  583 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7245 (pt)
REVERT: A  624 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7652 (t80)
REVERT: B   33 ASP cc_start: 0.7651 (t0) cc_final: 0.7282 (t0)
REVERT: B  213 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7056 (pp)
REVERT: B  220 ARG cc_start: 0.7721 (mtt-85) cc_final: 0.7418 (mtm-85)
REVERT: B  237 ASP cc_start: 0.8200 (m-30) cc_final: 0.7861 (m-30)
REVERT: B  513 MET cc_start: 0.5539 (ttp) cc_final: 0.5121 (ttp)
REVERT: B  517 TRP cc_start: 0.7468 (m100) cc_final: 0.6421 (t60)
REVERT: B  613 TYR cc_start: 0.5092 (OUTLIER) cc_final: 0.4500 (p90)
REVERT: B  628 LYS cc_start: 0.3688 (tttt) cc_final: 0.3409 (ttpt)
REVERT: B  664 PHE cc_start: 0.8637 (m-10) cc_final: 0.8428 (m-80)
REVERT: C   81 TYR cc_start: 0.8247 (m-80) cc_final: 0.7607 (m-80)
REVERT: D   37 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8334 (mt-10)
  outliers start: 30
  outliers final: 14
  residues processed: 187
  average time/residue: 0.2549
  time to fit residues: 65.4668
Evaluate side-chains
  159 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  482 PHE
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain C residue   95 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0980
   chunk 122 optimal weight:    5.9990
   chunk 132 optimal weight:    7.9990
   chunk 109 optimal weight:    0.8980
   chunk 121 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 526 ASN
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 ASN
D  26 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11025  Z= 0.168
  Angle     :  0.496   9.097  14920  Z= 0.247
  Chirality :  0.039   0.197   1698
  Planarity :  0.003   0.048   1879
  Dihedral  :  3.643  51.478   1503
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.85 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  0.45 (0.23), residues: 1349
  helix:  1.78 (0.20), residues: 715
  sheet: -0.70 (0.35), residues: 190
  loop : -1.76 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 229 
 HIS   0.003   0.001   HIS A 510 
 PHE   0.021   0.001   PHE B  93 
 TYR   0.017   0.001   TYR B 507 
 ARG   0.010   0.000   ARG B  96 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 1.284 
Fit side-chains
REVERT: A   41 LEU cc_start: 0.8640 (tp) cc_final: 0.8233 (mp)
REVERT: A   66 ARG cc_start: 0.6773 (mmt-90) cc_final: 0.6261 (mmp80)
REVERT: A  165 GLN cc_start: 0.7485 (tp-100) cc_final: 0.7092 (tp40)
REVERT: A  480 MET cc_start: 0.8321 (tpp) cc_final: 0.8119 (mmm)
REVERT: A  624 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7741 (t80)
REVERT: B   33 ASP cc_start: 0.7740 (t0) cc_final: 0.7347 (t0)
REVERT: B  213 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7075 (pp)
REVERT: B  220 ARG cc_start: 0.7664 (mtt-85) cc_final: 0.7433 (mtm-85)
REVERT: B  513 MET cc_start: 0.5497 (ttp) cc_final: 0.5039 (ttp)
REVERT: B  517 TRP cc_start: 0.7426 (m100) cc_final: 0.6241 (t60)
REVERT: B  613 TYR cc_start: 0.5298 (OUTLIER) cc_final: 0.4524 (p90)
REVERT: B  664 PHE cc_start: 0.8536 (m-10) cc_final: 0.8302 (m-80)
REVERT: C   81 TYR cc_start: 0.8306 (m-80) cc_final: 0.7467 (m-80)
REVERT: C   88 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7874 (ttp80)
REVERT: D   37 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8349 (mt-10)
  outliers start: 25
  outliers final: 14
  residues processed: 166
  average time/residue: 0.2641
  time to fit residues: 60.2829
Evaluate side-chains
  155 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain A residue  630 PHE
Chi-restraints excluded: chain A residue  645 ARG
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  500 GLU
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0170
   chunk 13 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 82 optimal weight:    4.9990
   chunk 123 optimal weight:    5.9990
   chunk 130 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 116 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   overall best weight:    2.1422

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11025  Z= 0.378
  Angle     :  0.608  10.458  14920  Z= 0.305
  Chirality :  0.044   0.291   1698
  Planarity :  0.004   0.044   1879
  Dihedral  :  3.868  29.772   1500
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.53 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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 (0.23), residues: 1349
  helix:  1.71 (0.19), residues: 713
  sheet: -0.45 (0.36), residues: 188
  loop : -1.56 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 229 
 HIS   0.004   0.001   HIS A 294 
 PHE   0.021   0.002   PHE B  93 
 TYR   0.015   0.002   TYR B 507 
 ARG   0.007   0.001   ARG B 313 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 128
  time to evaluate  : 1.286 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.6838 (mmt-90) cc_final: 0.6456 (mmp80)
REVERT: A  165 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7205 (tp40)
REVERT: A  324 MET cc_start: 0.7495 (tmm) cc_final: 0.7247 (tmm)
REVERT: A  480 MET cc_start: 0.8375 (tpp) cc_final: 0.8080 (mmm)
REVERT: A  624 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.7937 (t80)
REVERT: B  213 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7323 (pp)
REVERT: B  220 ARG cc_start: 0.7754 (mtt-85) cc_final: 0.7492 (mtm-85)
REVERT: B  517 TRP cc_start: 0.7470 (m100) cc_final: 0.6448 (t60)
REVERT: B  613 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.4838 (p90)
REVERT: B  628 LYS cc_start: 0.3975 (tttt) cc_final: 0.3662 (mmmt)
REVERT: C   32 GLN cc_start: 0.8837 (mp10) cc_final: 0.8605 (mp10)
REVERT: C   81 TYR cc_start: 0.8498 (m-80) cc_final: 0.7847 (m-80)
REVERT: D   37 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8335 (mt-10)
  outliers start: 34
  outliers final: 18
  residues processed: 154
  average time/residue: 0.2494
  time to fit residues: 53.9301
Evaluate side-chains
  141 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain A residue  630 PHE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  500 GLU
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  111 ASP
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   94 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 111 optimal weight:    0.7980
   chunk 90 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.4855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11025  Z= 0.306
  Angle     :  0.572  11.625  14920  Z= 0.285
  Chirality :  0.042   0.237   1698
  Planarity :  0.004   0.047   1879
  Dihedral  :  3.841  30.570   1500
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.70 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  0.70 (0.23), residues: 1349
  helix:  1.90 (0.19), residues: 701
  sheet: -0.27 (0.37), residues: 188
  loop : -1.52 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 229 
 HIS   0.003   0.001   HIS B 438 
 PHE   0.020   0.002   PHE B  93 
 TYR   0.018   0.002   TYR B 507 
 ARG   0.004   0.000   ARG B 313 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 1.462 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.6822 (mmt-90) cc_final: 0.6231 (mmp80)
REVERT: A  165 GLN cc_start: 0.7588 (tp-100) cc_final: 0.7219 (tp40)
REVERT: A  454 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7173 (mm-40)
REVERT: A  480 MET cc_start: 0.8390 (tpp) cc_final: 0.8188 (mmm)
REVERT: A  624 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7788 (t80)
REVERT: B   50 ARG cc_start: 0.6848 (ttm110) cc_final: 0.6287 (ttm110)
REVERT: B  213 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7411 (pp)
REVERT: B  220 ARG cc_start: 0.7735 (mtt-85) cc_final: 0.7457 (mtm-85)
REVERT: B  237 ASP cc_start: 0.8349 (m-30) cc_final: 0.7947 (m-30)
REVERT: B  517 TRP cc_start: 0.7420 (m100) cc_final: 0.6409 (t60)
REVERT: B  613 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.5094 (p90)
REVERT: B  628 LYS cc_start: 0.3980 (tttt) cc_final: 0.3741 (mmmt)
REVERT: C   32 GLN cc_start: 0.8845 (mp10) cc_final: 0.8621 (mp10)
REVERT: C   50 GLU cc_start: 0.8457 (tt0) cc_final: 0.8252 (tt0)
REVERT: C   81 TYR cc_start: 0.8496 (m-80) cc_final: 0.7920 (m-80)
REVERT: D   37 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8201 (mt-10)
  outliers start: 34
  outliers final: 19
  residues processed: 150
  average time/residue: 0.2563
  time to fit residues: 53.4112
Evaluate side-chains
  138 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain A residue  630 PHE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  500 GLU
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  111 ASP
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   94 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 117 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 130 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 68 optimal weight:    1.9990
   chunk 125 optimal weight:    0.0970
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.4824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11025  Z= 0.195
  Angle     :  0.525  10.548  14920  Z= 0.259
  Chirality :  0.040   0.195   1698
  Planarity :  0.003   0.047   1879
  Dihedral  :  3.646  29.674   1500
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.63 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.00 (0.24), residues: 1349
  helix:  2.07 (0.20), residues: 708
  sheet: -0.14 (0.37), residues: 197
  loop : -1.30 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 229 
 HIS   0.003   0.001   HIS B 531 
 PHE   0.018   0.001   PHE B  93 
 TYR   0.017   0.001   TYR B 507 
 ARG   0.004   0.000   ARG B 313 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 1.178 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.6833 (mmt-90) cc_final: 0.6256 (mmp80)
REVERT: A  165 GLN cc_start: 0.7535 (tp-100) cc_final: 0.7188 (tp40)
REVERT: A  454 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7056 (mm-40)
REVERT: A  624 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7727 (t80)
REVERT: A  630 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8219 (t80)
REVERT: B   50 ARG cc_start: 0.6893 (ttm110) cc_final: 0.6294 (ttm110)
REVERT: B  213 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7427 (pp)
REVERT: B  220 ARG cc_start: 0.7750 (mtt-85) cc_final: 0.7430 (mtm-85)
REVERT: B  237 ASP cc_start: 0.8250 (m-30) cc_final: 0.7842 (m-30)
REVERT: B  515 THR cc_start: 0.8882 (t) cc_final: 0.8550 (m)
REVERT: B  517 TRP cc_start: 0.7406 (m100) cc_final: 0.6391 (t60)
REVERT: B  613 TYR cc_start: 0.6168 (OUTLIER) cc_final: 0.5047 (p90)
REVERT: C   81 TYR cc_start: 0.8503 (m-80) cc_final: 0.7918 (m-80)
REVERT: D   37 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8215 (mt-10)
  outliers start: 27
  outliers final: 18
  residues processed: 144
  average time/residue: 0.2358
  time to fit residues: 47.7102
Evaluate side-chains
  138 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain A residue  630 PHE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  500 GLU
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  111 ASP
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 130 optimal weight:    0.0170
   chunk 81 optimal weight:    0.0270
   chunk 79 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.9280

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

Flipped N/Q/H residues before XYZ refinement:
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11025  Z= 0.193
  Angle     :  0.531  10.610  14920  Z= 0.260
  Chirality :  0.040   0.355   1698
  Planarity :  0.003   0.047   1879
  Dihedral  :  3.609  29.957   1500
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.38 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.17 (0.24), residues: 1349
  helix:  2.16 (0.20), residues: 708
  sheet:  0.05 (0.37), residues: 196
  loop : -1.20 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 461 
 HIS   0.004   0.001   HIS B 531 
 PHE   0.017   0.001   PHE B  93 
 TYR   0.017   0.001   TYR B 507 
 ARG   0.004   0.000   ARG B 610 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 1.374 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.6853 (mmt-90) cc_final: 0.6286 (mmp80)
REVERT: A   82 MET cc_start: 0.8717 (ttm) cc_final: 0.8462 (ttp)
REVERT: A  165 GLN cc_start: 0.7550 (tp-100) cc_final: 0.7213 (tp40)
REVERT: A  324 MET cc_start: 0.7573 (tmm) cc_final: 0.7286 (tmm)
REVERT: A  454 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7009 (mm-40)
REVERT: A  624 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7631 (t80)
REVERT: B   50 ARG cc_start: 0.6893 (ttm110) cc_final: 0.6274 (ttm110)
REVERT: B  213 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7370 (pp)
REVERT: B  220 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.7423 (mtm-85)
REVERT: B  343 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7577 (mm-40)
REVERT: B  517 TRP cc_start: 0.7398 (m100) cc_final: 0.6371 (t60)
REVERT: B  613 TYR cc_start: 0.6184 (OUTLIER) cc_final: 0.4990 (p90)
REVERT: C   81 TYR cc_start: 0.8481 (m-80) cc_final: 0.7918 (m-80)
REVERT: D   37 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8215 (mt-10)
  outliers start: 26
  outliers final: 20
  residues processed: 139
  average time/residue: 0.2337
  time to fit residues: 46.5703
Evaluate side-chains
  139 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain A residue  630 PHE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  500 GLU
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0070
   chunk 102 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   overall best weight:    1.6004

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

Flipped N/Q/H residues before XYZ refinement:
A 526 ASN
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  26 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11025  Z= 0.288
  Angle     :  0.577  11.124  14920  Z= 0.282
  Chirality :  0.041   0.208   1698
  Planarity :  0.004   0.048   1879
  Dihedral  :  3.791  30.551   1500
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 12.96 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.09 (0.24), residues: 1349
  helix:  2.04 (0.19), residues: 710
  sheet:  0.06 (0.37), residues: 196
  loop : -1.16 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 229 
 HIS   0.003   0.001   HIS A 493 
 PHE   0.017   0.001   PHE B  93 
 TYR   0.021   0.001   TYR A 628 
 ARG   0.004   0.000   ARG B 610 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 1.476 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.6903 (mmt-90) cc_final: 0.6346 (mmp80)
REVERT: A  165 GLN cc_start: 0.7592 (tp-100) cc_final: 0.7273 (tp40)
REVERT: A  454 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7072 (mm-40)
REVERT: A  624 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7767 (t80)
REVERT: B   50 ARG cc_start: 0.6902 (ttm110) cc_final: 0.6222 (ttm110)
REVERT: B  213 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7435 (pp)
REVERT: B  220 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.7416 (mtm-85)
REVERT: B  237 ASP cc_start: 0.8341 (m-30) cc_final: 0.7910 (m-30)
REVERT: B  343 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7586 (mm-40)
REVERT: B  517 TRP cc_start: 0.7408 (m100) cc_final: 0.6396 (t60)
REVERT: B  613 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5132 (p90)
REVERT: C   81 TYR cc_start: 0.8524 (m-80) cc_final: 0.7978 (m-80)
REVERT: D   37 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8150 (mt-10)
  outliers start: 30
  outliers final: 23
  residues processed: 141
  average time/residue: 0.2398
  time to fit residues: 48.2181
Evaluate side-chains
  143 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain A residue  630 PHE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  500 GLU
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  111 ASP
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 121 optimal weight:   10.0000
   chunk 124 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 95 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 109 optimal weight:    0.7980
   chunk 114 optimal weight:    0.8980
   chunk 120 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 526 ASN
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.4914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11025  Z= 0.162
  Angle     :  0.525  10.707  14920  Z= 0.254
  Chirality :  0.039   0.202   1698
  Planarity :  0.003   0.048   1879
  Dihedral  :  3.575  29.824   1500
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.55 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.32 (0.24), residues: 1349
  helix:  2.24 (0.20), residues: 708
  sheet:  0.17 (0.38), residues: 196
  loop : -1.09 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 461 
 HIS   0.004   0.001   HIS B 531 
 PHE   0.016   0.001   PHE B  93 
 TYR   0.018   0.001   TYR B 507 
 ARG   0.003   0.000   ARG B 610 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 1.214 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.6896 (mmt-90) cc_final: 0.6169 (mmp80)
REVERT: A   82 MET cc_start: 0.8700 (ttm) cc_final: 0.8443 (ttp)
REVERT: A  165 GLN cc_start: 0.7593 (tp-100) cc_final: 0.7286 (tp40)
REVERT: A  324 MET cc_start: 0.7578 (tmm) cc_final: 0.7309 (tmm)
REVERT: A  454 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.6936 (mm-40)
REVERT: A  624 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7560 (t80)
REVERT: B   50 ARG cc_start: 0.6901 (ttm110) cc_final: 0.6251 (ttm110)
REVERT: B  213 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7372 (pp)
REVERT: B  220 ARG cc_start: 0.7767 (mtt-85) cc_final: 0.7381 (mtm-85)
REVERT: B  343 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7563 (mm-40)
REVERT: B  517 TRP cc_start: 0.7421 (m100) cc_final: 0.6383 (t60)
REVERT: B  613 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5079 (p90)
REVERT: C   81 TYR cc_start: 0.8502 (m-80) cc_final: 0.7919 (m-80)
REVERT: D   37 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8162 (mt-10)
  outliers start: 29
  outliers final: 20
  residues processed: 142
  average time/residue: 0.2372
  time to fit residues: 47.7510
Evaluate side-chains
  141 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  500 GLU
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  111 ASP
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 128 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 134 optimal weight:    0.8980
   chunk 123 optimal weight:    7.9990
   chunk 107 optimal weight:    0.6980
   chunk 11 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 526 ASN
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.5210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11025  Z= 0.369
  Angle     :  0.622  11.524  14920  Z= 0.304
  Chirality :  0.043   0.215   1698
  Planarity :  0.004   0.048   1879
  Dihedral  :  3.931  30.866   1500
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.97 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.06 (0.24), residues: 1349
  helix:  2.03 (0.19), residues: 703
  sheet:  0.07 (0.38), residues: 196
  loop : -1.18 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 584 
 HIS   0.004   0.001   HIS B 438 
 PHE   0.018   0.002   PHE B  93 
 TYR   0.021   0.002   TYR A 628 
 ARG   0.004   0.000   ARG B 610 

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 1.213 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.6941 (mmt-90) cc_final: 0.6214 (mmp80)
REVERT: A  165 GLN cc_start: 0.7636 (tp-100) cc_final: 0.7336 (tp40)
REVERT: A  454 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7075 (mm-40)
REVERT: A  624 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7838 (t80)
REVERT: B  213 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7508 (pp)
REVERT: B  220 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7444 (mtm-85)
REVERT: B  237 ASP cc_start: 0.8388 (m-30) cc_final: 0.7961 (m-30)
REVERT: B  343 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7533 (mm-40)
REVERT: B  517 TRP cc_start: 0.7472 (m100) cc_final: 0.6427 (t60)
REVERT: B  613 TYR cc_start: 0.6528 (OUTLIER) cc_final: 0.5106 (p90)
REVERT: C   81 TYR cc_start: 0.8565 (m-80) cc_final: 0.8147 (m-80)
REVERT: D   37 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8055 (mt-10)
  outliers start: 26
  outliers final: 22
  residues processed: 141
  average time/residue: 0.2494
  time to fit residues: 49.1421
Evaluate side-chains
  143 residues out of total 1181 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain A residue  630 PHE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  500 GLU
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  111 ASP
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0770
   chunk 19 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.125235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.102640 restraints weight = 14040.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 1.78
r_work: 0.2887 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.5021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11025  Z= 0.165
  Angle     :  0.538  10.847  14920  Z= 0.259
  Chirality :  0.039   0.201   1698
  Planarity :  0.003   0.048   1879
  Dihedral  :  3.637  30.295   1500
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.39 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.34 (0.24), residues: 1349
  helix:  2.29 (0.20), residues: 703
  sheet:  0.19 (0.38), residues: 196
  loop : -1.09 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 229 
 HIS   0.004   0.001   HIS B 531 
 PHE   0.016   0.001   PHE B  93 
 TYR   0.022   0.001   TYR B 507 
 ARG   0.005   0.000   ARG B 610 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2370.79 seconds
wall clock time: 43 minutes 37.89 seconds (2617.89 seconds total)