Starting phenix.real_space_refine
on Sun Mar 10 23:06:37 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/03_2024/7bh9_12187.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/03_2024/7bh9_12187.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/03_2024/7bh9_12187.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/03_2024/7bh9_12187.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/03_2024/7bh9_12187.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/03_2024/7bh9_12187.pdb"
  }
  resolution = 2.9
  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
-------------------------------------------------------------------------------
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=   0.037
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      34      5.16       5
     C    3787      2.51       5
     N     970      2.21       5
     O    1084      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   83": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  115": "NH1" <-> "NH2"
    Residue "A TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  169": "NH1" <-> "NH2"
    Residue "A ARG  177": "NH1" <-> "NH2"
    Residue "A ARG  192": "NH1" <-> "NH2"
    Residue "A ASP  206": "OD1" <-> "OD2"
    Residue "A TYR  217": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  224": "OE1" <-> "OE2"
    Residue "A GLU  231": "OE1" <-> "OE2"
    Residue "A ARG  245": "NH1" <-> "NH2"
    Residue "A ARG  273": "NH1" <-> "NH2"
    Residue "A ASP  295": "OD1" <-> "OD2"
    Residue "A PHE  308": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  327": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  357": "NH1" <-> "NH2"
    Residue "A TYR  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  390": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  402": "OE1" <-> "OE2"
    Residue "A PHE  428": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  452": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  489": "OE1" <-> "OE2"
    Residue "A ARG  518": "NH1" <-> "NH2"
    Residue "A GLU  564": "OE1" <-> "OE2"
    Residue "A TYR  587": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  597": "OD1" <-> "OD2"
    Residue "A TYR  613": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 5876
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 586, 4704
          Classifications: {'peptide': 586}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 560}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 63
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 66
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1129
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 7, 'TRANS': 136}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.87, per 1000 atoms: 0.66
  Number of scatterers: 5876
  At special positions: 0
  Unit cell: (68.77, 81.466, 111.09, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      34     16.00
     O    1084      8.00
     N     970      7.00
     C    3787      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=1.99

  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
  Links applied
    NAG-ASN
      " NAG A 902 " - " ASN A 546 "
      " NAG A 903 " - " ASN A  90 "
      " NAG A 904 " - " ASN A  53 "
  Time building additional restraints: 2.30
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "


  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1372

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      58.1% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.676A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN A  53 " --> pdb=" O   ASN A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 81
      removed outlier: 3.596A  pdb=" N   ASN A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 4.009A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 129
      removed outlier: 3.507A  pdb=" N   TYR A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 154
    Processing helix  chain 'A' and resid 157 through 172
      removed outlier: 3.622A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 193
      Proline residue:  A 178  - end of helix
      removed outlier: 3.708A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 221 through 252
      removed outlier: 3.799A  pdb=" N   GLU A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 4.168A  pdb=" N   ILE A 256 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 253 through 256'
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 282
      removed outlier: 4.630A  pdb=" N   SER A 280 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 299
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.837A  pdb=" N   ILE A 307 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.639A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 385
      removed outlier: 3.890A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.993A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 4.044A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 433 through 447
      removed outlier: 3.910A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE A 438 " --> pdb=" O   THR A 434 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU A 439 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 481
      removed outlier: 3.667A  pdb=" N   TRP A 478 " --> pdb=" O   MET A 474 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
      removed outlier: 3.536A  pdb=" N   SER A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.114A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 3.838A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   LEU A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.895A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
      removed outlier: 3.755A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'E' and resid 403 through 410
      removed outlier: 3.630A  pdb=" N   GLU E 406 " --> pdb=" O   ARG E 403 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 417 through 422
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.988A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'E' and resid 376 through 379
    Processing sheet with id=AA5, first strand: chain 'E' and resid 448 through 454
      removed outlier: 6.095A  pdb=" N   TYR E 449 " --> pdb=" O   PHE E 497 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   PHE E 497 " --> pdb=" O   TYR E 449 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TYR E 451 " --> pdb=" O   TYR E 495 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474

    271 hydrogen bonds defined for protein.
    747 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: 1.54

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1248
        1.33 -     1.45: 1531
        1.45 -     1.57: 3206
        1.57 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 6041
  Sorted by residual:
  bond pdb=" CA  SER A 331 "
       pdb=" CB  SER A 331 "
    ideal  model  delta    sigma   weight residual
    1.530  1.472  0.058 1.55e-02 4.16e+03 1.40e+01
  bond pdb=" C   THR E 478 "
       pdb=" N   PRO E 479 "
    ideal  model  delta    sigma   weight residual
    1.330  1.372 -0.042 1.25e-02 6.40e+03 1.14e+01
  bond pdb=" N   VAL E 483 "
       pdb=" CA  VAL E 483 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.15e-02 7.56e+03 8.70e+00
  bond pdb=" N   SER A 331 "
       pdb=" CA  SER A 331 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.22e-02 6.72e+03 6.28e+00
  bond pdb=" C   GLU A  22 "
       pdb=" O   GLU A  22 "
    ideal  model  delta    sigma   weight residual
    1.236  1.207  0.029 1.19e-02 7.06e+03 5.92e+00
  ... (remaining 6036 not shown)

  Histogram of bond angle deviations from ideal:
       99.72 -   106.59: 182
      106.59 -   113.46: 3137
      113.46 -   120.33: 2409
      120.33 -   127.20: 2388
      127.20 -   134.07: 93
  Bond angle restraints: 8209
  Sorted by residual:
  angle pdb=" N   ASN E 481 "
        pdb=" CA  ASN E 481 "
        pdb=" C   ASN E 481 "
      ideal   model   delta    sigma   weight residual
     112.97  104.76    8.21 1.06e+00 8.90e-01 6.00e+01
  angle pdb=" N   GLY E 482 "
        pdb=" CA  GLY E 482 "
        pdb=" C   GLY E 482 "
      ideal   model   delta    sigma   weight residual
     115.30  106.84    8.46 1.39e+00 5.18e-01 3.71e+01
  angle pdb=" N   PRO E 479 "
        pdb=" CA  PRO E 479 "
        pdb=" C   PRO E 479 "
      ideal   model   delta    sigma   weight residual
     111.22  118.06   -6.84 1.40e+00 5.10e-01 2.39e+01
  angle pdb=" CA  CYS E 480 "
        pdb=" C   CYS E 480 "
        pdb=" N   ASN E 481 "
      ideal   model   delta    sigma   weight residual
     115.51  120.83   -5.32 1.24e+00 6.50e-01 1.84e+01
  angle pdb=" C   ASN A 330 "
        pdb=" CA  ASN A 330 "
        pdb=" CB  ASN A 330 "
      ideal   model   delta    sigma   weight residual
     111.02  104.86    6.16 1.62e+00 3.81e-01 1.44e+01
  ... (remaining 8204 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.40: 3210
       16.40 -    32.79: 282
       32.79 -    49.19: 52
       49.19 -    65.58: 16
       65.58 -    81.98: 4
  Dihedral angle restraints: 3564
    sinusoidal: 1426
      harmonic: 2138
  Sorted by residual:
  dihedral pdb=" CB  CYS E 480 "
           pdb=" SG  CYS E 480 "
           pdb=" SG  CYS E 488 "
           pdb=" CB  CYS E 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.93   35.93     1      1.00e+01 1.00e-02 1.83e+01
  dihedral pdb=" CA  TYR A 252 "
           pdb=" C   TYR A 252 "
           pdb=" N   PRO A 253 "
           pdb=" CA  PRO A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.11  -18.89     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  PRO A 389 "
           pdb=" C   PRO A 389 "
           pdb=" N   PHE A 390 "
           pdb=" CA  PHE A 390 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.32  -17.68     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 3561 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 652
       0.053 -    0.105: 187
       0.105 -    0.158: 31
       0.158 -    0.210: 1
       0.210 -    0.263: 2
  Chirality restraints: 873
  Sorted by residual:
  chirality pdb=" CA  ASN E 481 "
            pdb=" N   ASN E 481 "
            pdb=" C   ASN E 481 "
            pdb=" CB  ASN E 481 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  PRO E 479 "
            pdb=" N   PRO E 479 "
            pdb=" C   PRO E 479 "
            pdb=" CB  PRO E 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CB  ILE A  21 "
            pdb=" CA  ILE A  21 "
            pdb=" CG1 ILE A  21 "
            pdb=" CG2 ILE A  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 6.86e-01
  ... (remaining 870 not shown)

  Planarity restraints: 1049
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 495 "    0.023 2.00e-02 2.50e+03   1.35e-02 3.67e+00
        pdb=" CG  TYR E 495 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 495 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 495 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 495 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 495 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 495 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR E 495 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  21 "    0.009 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" C   ILE A  21 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ILE A  21 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A  22 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 234 "   -0.031 5.00e-02 4.00e+02   4.61e-02 3.40e+00
        pdb=" N   PRO A 235 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 235 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 235 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1046 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 37
        2.60 -     3.17: 4671
        3.17 -     3.75: 8205
        3.75 -     4.32: 12466
        4.32 -     4.90: 21205
  Nonbonded interactions: 46584
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 901 "
     model   vdw
     2.021 2.230
  nonbonded pdb=" OG  SER A  19 "
            pdb=" OE1 GLU A  23 "
     model   vdw
     2.175 2.440
  nonbonded pdb=" O   SER E 438 "
            pdb=" OG  SER E 438 "
     model   vdw
     2.247 2.440
  nonbonded pdb=" OH  TYR A 217 "
            pdb=" OD2 ASP A 225 "
     model   vdw
     2.284 2.440
  nonbonded pdb=" OE2 GLU A 435 "
            pdb=" NZ  LYS A 541 "
     model   vdw
     2.289 2.520
  ... (remaining 46579 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:             3.400
  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:          8.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.060
  Process input model:                     21.730
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  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:11.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
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      :  0.007   0.058   6041  Z= 0.447
  Angle     :  0.767   8.974   8209  Z= 0.444
  Chirality :  0.050   0.263    873
  Planarity :  0.005   0.046   1046
  Dihedral  : 13.182  81.978   2183
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  3.98 %
    Favored  : 95.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.10 (0.27), residues: 718
  helix: -1.42 (0.24), residues: 375
  sheet: -2.04 (0.69), residues: 41
  loop : -2.83 (0.28), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 353 
 HIS   0.010   0.001   HIS A 241 
 PHE   0.014   0.002   PHE A 512 
 TYR   0.030   0.002   TYR E 495 
 ARG   0.002   0.000   ARG A 393 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 67
  average time/residue: 1.1329
  time to fit residues: 80.2047
Evaluate side-chains
  49 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue  597 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.0980
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN
A 374 HIS
A 380 GLN
E 354 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6041  Z= 0.143
  Angle     :  0.491   5.293   8209  Z= 0.259
  Chirality :  0.040   0.128    873
  Planarity :  0.004   0.031   1046
  Dihedral  :  4.963  43.775    857
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 10.12 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.46 (0.30), residues: 718
  helix:  0.05 (0.28), residues: 371
  sheet: -1.06 (0.66), residues: 49
  loop : -2.27 (0.29), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.009   0.001   PHE E 377 
 TYR   0.018   0.001   TYR E 495 
 ARG   0.002   0.000   ARG A 559 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
REVERT: A  455 MET cc_start: 0.8877 (tmm) cc_final: 0.8643 (tmt)
REVERT: E  408 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7286 (ptm160)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 1.0940
  time to fit residues: 66.1059
Evaluate side-chains
  51 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain E residue  408 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0570
   chunk 18 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0370
   chunk 70 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.5776

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
E 354 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6041  Z= 0.124
  Angle     :  0.446   5.274   8209  Z= 0.232
  Chirality :  0.038   0.131    873
  Planarity :  0.003   0.029   1046
  Dihedral  :  4.115  35.903    855
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 11.77 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.63 (0.31), residues: 718
  helix:  0.65 (0.28), residues: 380
  sheet: -0.43 (0.81), residues: 37
  loop : -1.84 (0.30), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.008   0.001   PHE E 342 
 TYR   0.016   0.001   TYR E 495 
 ARG   0.001   0.000   ARG A 482 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8440 (m)
REVERT: E  408 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7291 (ptm160)
  outliers start: 4
  outliers final: 2
  residues processed: 59
  average time/residue: 1.0684
  time to fit residues: 66.7703
Evaluate side-chains
  54 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  469 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 7 optimal weight:    0.5980
   chunk 31 optimal weight:    9.9990
   chunk 43 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6041  Z= 0.152
  Angle     :  0.459   5.336   8209  Z= 0.239
  Chirality :  0.039   0.131    873
  Planarity :  0.003   0.029   1046
  Dihedral  :  3.916  27.606    855
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 12.94 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.31), residues: 718
  helix:  1.08 (0.29), residues: 374
  sheet: -0.02 (0.85), residues: 37
  loop : -1.69 (0.31), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.009   0.001   PHE A 452 
 TYR   0.021   0.001   TYR E 495 
 ARG   0.001   0.000   ARG A 482 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8454 (m)
REVERT: E  408 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7327 (ptm160)
  outliers start: 7
  outliers final: 3
  residues processed: 54
  average time/residue: 1.1646
  time to fit residues: 66.5304
Evaluate side-chains
  54 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  503 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    0.0060
   chunk 39 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0470
   chunk 48 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.2098

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6041  Z= 0.163
  Angle     :  0.458   5.397   8209  Z= 0.238
  Chirality :  0.039   0.131    873
  Planarity :  0.003   0.028   1046
  Dihedral  :  3.754  24.216    854
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.43 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.05 (0.32), residues: 718
  helix:  1.24 (0.29), residues: 375
  sheet:  0.10 (0.87), residues: 37
  loop : -1.55 (0.31), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 452 
 TYR   0.019   0.001   TYR E 495 
 ARG   0.001   0.000   ARG A 482 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8454 (m)
  outliers start: 8
  outliers final: 4
  residues processed: 53
  average time/residue: 1.1710
  time to fit residues: 65.7119
Evaluate side-chains
  54 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain E residue  354 ASN
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  503 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0030
   chunk 17 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0770
   chunk 57 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    1.1550

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6041  Z= 0.159
  Angle     :  0.456   5.396   8209  Z= 0.236
  Chirality :  0.039   0.131    873
  Planarity :  0.003   0.028   1046
  Dihedral  :  3.700  22.511    854
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 13.76 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.32), residues: 718
  helix:  1.37 (0.29), residues: 375
  sheet:  0.33 (0.88), residues: 37
  loop : -1.45 (0.32), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.007   0.001   PHE A 327 
 TYR   0.019   0.001   TYR E 495 
 ARG   0.001   0.000   ARG A 482 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8464 (m)
  outliers start: 7
  outliers final: 3
  residues processed: 59
  average time/residue: 1.2373
  time to fit residues: 76.9220
Evaluate side-chains
  55 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain E residue  375 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0070
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.4004

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6041  Z= 0.182
  Angle     :  0.474   5.448   8209  Z= 0.245
  Chirality :  0.040   0.131    873
  Planarity :  0.003   0.027   1046
  Dihedral  :  3.729  21.935    854
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.43 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.32), residues: 718
  helix:  1.41 (0.29), residues: 375
  sheet:  0.43 (0.90), residues: 37
  loop : -1.39 (0.32), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 523 
 TYR   0.021   0.001   TYR E 495 
 ARG   0.001   0.000   ARG A 482 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8463 (m)
REVERT: E  460 LYS cc_start: 0.9192 (mttt) cc_final: 0.8975 (mttm)
  outliers start: 10
  outliers final: 6
  residues processed: 61
  average time/residue: 1.2300
  time to fit residues: 79.3633
Evaluate side-chains
  59 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  503 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 GLN
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6041  Z= 0.277
  Angle     :  0.528   5.819   8209  Z= 0.275
  Chirality :  0.042   0.139    873
  Planarity :  0.003   0.028   1046
  Dihedral  :  3.980  19.323    854
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.93 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.12 (0.32), residues: 718
  helix:  1.13 (0.28), residues: 382
  sheet:  0.05 (0.77), residues: 47
  loop : -1.37 (0.34), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.010   0.001   PHE A 327 
 TYR   0.024   0.001   TYR E 495 
 ARG   0.001   0.000   ARG A 482 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8459 (m)
REVERT: A  325 GLN cc_start: 0.7825 (tp40) cc_final: 0.7364 (tm-30)
REVERT: E  460 LYS cc_start: 0.9194 (mttt) cc_final: 0.8980 (mttm)
  outliers start: 13
  outliers final: 8
  residues processed: 59
  average time/residue: 1.2021
  time to fit residues: 74.8275
Evaluate side-chains
  60 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  503 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 64 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0010
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6041  Z= 0.132
  Angle     :  0.454   6.344   8209  Z= 0.233
  Chirality :  0.039   0.132    873
  Planarity :  0.003   0.027   1046
  Dihedral  :  3.663  22.825    854
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.10 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.32), residues: 718
  helix:  1.55 (0.29), residues: 375
  sheet:  0.63 (0.91), residues: 37
  loop : -1.27 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.008   0.001   PHE E 342 
 TYR   0.016   0.001   TYR E 495 
 ARG   0.001   0.000   ARG A 219 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8485 (m)
REVERT: E  460 LYS cc_start: 0.9191 (mttt) cc_final: 0.8937 (mttm)
  outliers start: 10
  outliers final: 8
  residues processed: 64
  average time/residue: 1.2918
  time to fit residues: 86.9454
Evaluate side-chains
  62 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 60 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  98 GLN
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6041  Z= 0.332
  Angle     :  0.564   7.370   8209  Z= 0.292
  Chirality :  0.044   0.145    873
  Planarity :  0.004   0.028   1046
  Dihedral  :  4.052  17.300    854
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.76 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.19 (0.32), residues: 718
  helix:  1.22 (0.28), residues: 380
  sheet:  0.04 (0.75), residues: 49
  loop : -1.34 (0.34), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.011   0.001   PHE A 327 
 TYR   0.025   0.002   TYR E 495 
 ARG   0.002   0.000   ARG A 357 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8452 (m)
REVERT: A  325 GLN cc_start: 0.7862 (tp40) cc_final: 0.7442 (tm-30)
REVERT: E  460 LYS cc_start: 0.9204 (mttt) cc_final: 0.8991 (mttm)
  outliers start: 9
  outliers final: 7
  residues processed: 56
  average time/residue: 1.2591
  time to fit residues: 74.4347
Evaluate side-chains
  58 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  459 SER
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.092055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.076398 restraints weight = 10111.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.81
r_work: 0.2867 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6041  Z= 0.219
  Angle     :  0.508   7.456   8209  Z= 0.262
  Chirality :  0.041   0.133    873
  Planarity :  0.003   0.027   1046
  Dihedral  :  3.914  20.616    854
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.26 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.32), residues: 718
  helix:  1.36 (0.28), residues: 379
  sheet:  0.20 (0.77), residues: 47
  loop : -1.30 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.009   0.001   PHE A 327 
 TYR   0.021   0.001   TYR E 495 
 ARG   0.001   0.000   ARG A 273 

===============================================================================
Job complete
usr+sys time: 2100.49 seconds
wall clock time: 38 minutes 20.01 seconds (2300.01 seconds total)