Starting phenix.real_space_refine
on Sat May 10 13:55:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hrk_34976/05_2025/8hrk_34976.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hrk_34976/05_2025/8hrk_34976.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hrk_34976/05_2025/8hrk_34976.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hrk_34976/05_2025/8hrk_34976.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hrk_34976/05_2025/8hrk_34976.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hrk_34976/05_2025/8hrk_34976.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.157
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      37      5.16       5
     C    4101      2.51       5
     N    1066      2.21       5
     O    1208      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6412
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
    Chain: "E"
      Number of atoms: 1542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1542
          Classifications: {'peptide': 194}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183}
  Time building chain proxies: 4.54, per 1000 atoms: 0.71
  Number of scatterers: 6412
  At special positions: 0
  Unit cell: (71.38, 88.58, 126.42, 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      37     16.00
     O    1208      8.00
     N    1066      7.00
     C    4101      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    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 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 955.4 milliseconds
  

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1488

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      48.2% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.720A  pdb=" N   LYS A  26 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   TYR A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 80
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 90 through 99
      removed outlier: 3.592A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.823A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.740A  pdb=" N   SER A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 152
      removed outlier: 3.669A  pdb=" N   MET A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 169
      removed outlier: 3.577A  pdb=" N   ALA A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TRP A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 193
      removed outlier: 3.549A  pdb=" N   ALA A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 218 through 220
      No H-bonds generated for 'chain 'A' and resid 218 through 220'
    Processing helix  chain 'A' and resid 221 through 248
      removed outlier: 3.881A  pdb=" N   GLU A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE A 233 " --> pdb=" O   THR A 229 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 249 through 251
      No H-bonds generated for 'chain 'A' and resid 249 through 251'
    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 279
    Processing helix  chain 'A' and resid 293 through 299
      removed outlier: 3.560A  pdb=" N   VAL A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ASP A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 4.248A  pdb=" N   LYS A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   PHE A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY A 319 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 330
      removed outlier: 4.247A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASN A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 325 through 330'
    Processing helix  chain 'A' and resid 365 through 383
      removed outlier: 3.633A  pdb=" N   THR A 371 " --> pdb=" O   ASP A 367 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 413
      removed outlier: 3.543A  pdb=" N   LEU A 410 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.733A  pdb=" N   ILE A 436 " --> pdb=" O   ASN A 432 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 446 " --> pdb=" O   GLN A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 465
      removed outlier: 3.525A  pdb=" N   LYS A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 482
      removed outlier: 4.168A  pdb=" N   TRP A 478 " --> pdb=" O   MET A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.547A  pdb=" N   ARG A 518 " --> pdb=" O   ARG A 514 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.747A  pdb=" N   CYS A 542 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 4.078A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ASN A 556 " --> pdb=" O   GLN A 552 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 572
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
      removed outlier: 3.749A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 338 through 343
    Processing helix  chain 'E' and resid 365 through 370
      removed outlier: 3.767A  pdb=" N   TYR E 369 " --> pdb=" O   TYR E 365 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ASN E 370 " --> pdb=" O   SER E 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 365 through 370'
    Processing helix  chain 'E' and resid 385 through 389
      removed outlier: 3.977A  pdb=" N   ASN E 388 " --> pdb=" O   THR E 385 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASP E 389 " --> pdb=" O   LYS E 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 385 through 389'
    Processing helix  chain 'E' and resid 406 through 410
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.451A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352
      removed outlier: 3.938A  pdb=" N   TRP A 349 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.537A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU E 516 " --> pdb=" O   ASN E 394 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR E 396 " --> pdb=" O   SER E 514 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE E 402 " --> pdb=" O   TYR E 508 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL E 511 " --> pdb=" O   ILE E 434 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE E 434 " --> pdb=" O   VAL E 511 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS E 378 " --> pdb=" O   VAL E 433 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474
      removed outlier: 3.767A  pdb=" N   TYR E 489 " --> pdb=" O   TYR E 473 " (cutoff:3.500A)

    211 hydrogen bonds defined for protein.
    597 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: 1.81

  Time building geometry restraints manager: 1.88 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: 1286
        1.33 -     1.45: 1729
        1.45 -     1.57: 3516
        1.57 -     1.69: 3
        1.69 -     1.81: 58
  Bond restraints: 6592
  Sorted by residual:
  bond pdb=" CG  PRO A 415 "
       pdb=" CD  PRO A 415 "
    ideal  model  delta    sigma   weight residual
    1.503  1.208  0.295 3.40e-02 8.65e+02 7.55e+01
  bond pdb=" N   PRO A 415 "
       pdb=" CD  PRO A 415 "
    ideal  model  delta    sigma   weight residual
    1.473  1.530 -0.057 1.40e-02 5.10e+03 1.64e+01
  bond pdb=" CB  PRO A 235 "
       pdb=" CG  PRO A 235 "
    ideal  model  delta    sigma   weight residual
    1.492  1.654 -0.162 5.00e-02 4.00e+02 1.05e+01
  bond pdb=" CB  PRO A 415 "
       pdb=" CG  PRO A 415 "
    ideal  model  delta    sigma   weight residual
    1.492  1.630 -0.138 5.00e-02 4.00e+02 7.59e+00
  bond pdb=" CG  PRO A 235 "
       pdb=" CD  PRO A 235 "
    ideal  model  delta    sigma   weight residual
    1.503  1.416  0.087 3.40e-02 8.65e+02 6.52e+00
  ... (remaining 6587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.56: 8926
        3.56 -     7.12: 25
        7.12 -    10.68: 3
       10.68 -    14.24: 2
       14.24 -    17.80: 2
  Bond angle restraints: 8958
  Sorted by residual:
  angle pdb=" CA  PRO A 235 "
        pdb=" N   PRO A 235 "
        pdb=" CD  PRO A 235 "
      ideal   model   delta    sigma   weight residual
     112.00   94.20   17.80 1.40e+00 5.10e-01 1.62e+02
  angle pdb=" N   PRO A 415 "
        pdb=" CD  PRO A 415 "
        pdb=" CG  PRO A 415 "
      ideal   model   delta    sigma   weight residual
     103.20   85.48   17.72 1.50e+00 4.44e-01 1.40e+02
  angle pdb=" CA  PRO A 415 "
        pdb=" N   PRO A 415 "
        pdb=" CD  PRO A 415 "
      ideal   model   delta    sigma   weight residual
     112.00   98.48   13.52 1.40e+00 5.10e-01 9.33e+01
  angle pdb=" N   PRO A 235 "
        pdb=" CD  PRO A 235 "
        pdb=" CG  PRO A 235 "
      ideal   model   delta    sigma   weight residual
     103.20   93.98    9.22 1.50e+00 4.44e-01 3.77e+01
  angle pdb=" CA  PRO A 415 "
        pdb=" CB  PRO A 415 "
        pdb=" CG  PRO A 415 "
      ideal   model   delta    sigma   weight residual
     104.50   92.97   11.53 1.90e+00 2.77e-01 3.68e+01
  ... (remaining 8953 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 3337
       18.00 -    36.00: 432
       36.00 -    53.99: 97
       53.99 -    71.99: 19
       71.99 -    89.99: 8
  Dihedral angle restraints: 3893
    sinusoidal: 1573
      harmonic: 2320
  Sorted by residual:
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.81  -83.81     1      1.00e+01 1.00e-02 8.57e+01
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.88  -54.88     1      1.00e+01 1.00e-02 4.08e+01
  dihedral pdb=" CB  CYS E 336 "
           pdb=" SG  CYS E 336 "
           pdb=" SG  CYS E 361 "
           pdb=" CB  CYS E 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -44.04  -41.96     1      1.00e+01 1.00e-02 2.46e+01
  ... (remaining 3890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 414
       0.024 -    0.049: 319
       0.049 -    0.073: 142
       0.073 -    0.097: 35
       0.097 -    0.121: 24
  Chirality restraints: 934
  Sorted by residual:
  chirality pdb=" CA  VAL E 511 "
            pdb=" N   VAL E 511 "
            pdb=" C   VAL E 511 "
            pdb=" CB  VAL E 511 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.68e-01
  chirality pdb=" CA  ILE A 358 "
            pdb=" N   ILE A 358 "
            pdb=" C   ILE A 358 "
            pdb=" CB  ILE A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  chirality pdb=" CA  PRO A 415 "
            pdb=" N   PRO A 415 "
            pdb=" C   PRO A 415 "
            pdb=" CB  PRO A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.11 2.00e-01 2.50e+01 3.22e-01
  ... (remaining 931 not shown)

  Planarity restraints: 1165
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 234 "   -0.106 5.00e-02 4.00e+02   1.45e-01 3.34e+01
        pdb=" N   PRO A 235 "    0.249 5.00e-02 4.00e+02
        pdb=" CA  PRO A 235 "   -0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO A 235 "   -0.075 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 320 "    0.082 5.00e-02 4.00e+02   1.21e-01 2.35e+01
        pdb=" N   PRO A 321 "   -0.210 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "    0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "    0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 414 "    0.063 5.00e-02 4.00e+02   8.70e-02 1.21e+01
        pdb=" N   PRO A 415 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A 415 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 415 "    0.047 5.00e-02 4.00e+02
  ... (remaining 1162 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1697
        2.80 -     3.32: 5341
        3.32 -     3.85: 9886
        3.85 -     4.37: 11141
        4.37 -     4.90: 19953
  Nonbonded interactions: 48018
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG E 346 "
            pdb=" O   PHE E 347 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OE2 GLU A 489 "
            pdb=" OH  TYR A 613 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OH  TYR E 351 "
            pdb=" NH2 ARG E 452 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OG  SER E 371 "
            pdb=" OG  SER E 373 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   LEU A 333 "
            pdb=" OG1 THR A 362 "
     model   vdw
     2.293 3.040
  ... (remaining 48013 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.900
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     18.820
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
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      :  0.005   0.295   6599  Z= 0.192
  Angle     :  0.713  17.801   8972  Z= 0.445
  Chirality :  0.040   0.121    934
  Planarity :  0.008   0.145   1165
  Dihedral  : 16.730  89.990   2384
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 17.87 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -1.80 (0.29), residues: 787
  helix: -0.48 (0.29), residues: 345
  sheet: -2.36 (0.79), residues: 42
  loop : -1.69 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 349 
 HIS   0.001   0.000   HIS A 239 
 PHE   0.008   0.001   PHE A 369 
 TYR   0.018   0.001   TYR A  41 
 ARG   0.002   0.000   ARG A 460 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20776 (  211)
  hydrogen bonds       : angle       6.46196 (  597)
  SS BOND              : bond        0.00157 (    7)
  SS BOND              : angle       1.56305 (   14)
  covalent geometry    : bond        0.00538 ( 6592)
  covalent geometry    : angle       0.71052 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.6793 (tt0) cc_final: 0.6416 (mt-10)
REVERT: A  376 MET cc_start: 0.7200 (ttt) cc_final: 0.6910 (ttt)
REVERT: E  335 LEU cc_start: 0.0534 (OUTLIER) cc_final: -0.0132 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1882
  time to fit residues: 23.1637
Evaluate side-chains
  79 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  335 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 121 ASN
** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 HIS
A 380 GLN
A 432 ASN
E 474 GLN
E 493 GLN
E 498 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.182931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.149891 restraints weight = 7769.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.16
r_work: 0.3495 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.5272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067   6599  Z= 0.354
  Angle     :  0.913  11.283   8972  Z= 0.495
  Chirality :  0.055   0.231    934
  Planarity :  0.008   0.088   1165
  Dihedral  :  6.440  49.050    863
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 19.45 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -2.79 (0.26), residues: 787
  helix: -1.41 (0.26), residues: 341
  sheet: -1.58 (1.52), residues: 12
  loop : -2.28 (0.26), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.003   TRP A 473 
 HIS   0.020   0.003   HIS A 241 
 PHE   0.029   0.003   PHE A 230 
 TYR   0.028   0.003   TYR E 351 
 ARG   0.007   0.001   ARG A 245 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12246 (  211)
  hydrogen bonds       : angle       6.10338 (  597)
  SS BOND              : bond        0.00546 (    7)
  SS BOND              : angle       1.80091 (   14)
  covalent geometry    : bond        0.00833 ( 6592)
  covalent geometry    : angle       0.91059 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7882 (tt0) cc_final: 0.7380 (mt-10)
REVERT: A  167 SER cc_start: 0.8755 (t) cc_final: 0.7462 (m)
REVERT: A  171 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.5762 (mp0)
REVERT: A  432 ASN cc_start: 0.7676 (m110) cc_final: 0.6412 (t0)
REVERT: E  414 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6198 (mp10)
REVERT: E  442 ASP cc_start: 0.8021 (m-30) cc_final: 0.7809 (m-30)
  outliers start: 28
  outliers final: 10
  residues processed: 109
  average time/residue: 0.1830
  time to fit residues: 26.7188
Evaluate side-chains
  75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  494 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
A 380 GLN
A 401 HIS
E 493 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.187308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.149506 restraints weight = 7828.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.49
r_work: 0.3544 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.5265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6599  Z= 0.148
  Angle     :  0.559   5.281   8972  Z= 0.303
  Chirality :  0.043   0.192    934
  Planarity :  0.005   0.071   1165
  Dihedral  :  5.083  50.582    863
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.75 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -2.15 (0.28), residues: 787
  helix: -0.69 (0.28), residues: 339
  sheet: -1.89 (1.34), residues: 12
  loop : -2.07 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 473 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.016   0.002   PHE A 327 
 TYR   0.014   0.001   TYR E 495 
 ARG   0.002   0.000   ARG A 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06656 (  211)
  hydrogen bonds       : angle       4.98156 (  597)
  SS BOND              : bond        0.00203 (    7)
  SS BOND              : angle       0.75266 (   14)
  covalent geometry    : bond        0.00321 ( 6592)
  covalent geometry    : angle       0.55871 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5857 (pt0)
REVERT: A   75 GLU cc_start: 0.7157 (tp30) cc_final: 0.6895 (tp30)
REVERT: A  123 MET cc_start: 0.8106 (mtt) cc_final: 0.7886 (mtm)
REVERT: A  206 ASP cc_start: 0.7393 (t70) cc_final: 0.7173 (t0)
  outliers start: 15
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1726
  time to fit residues: 20.4168
Evaluate side-chains
  76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  335 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.175263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.141715 restraints weight = 7845.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.50
r_work: 0.3419 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.6536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   6599  Z= 0.291
  Angle     :  0.728   7.933   8972  Z= 0.395
  Chirality :  0.050   0.208    934
  Planarity :  0.006   0.069   1165
  Dihedral  :  5.759  49.262    863
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 20.03 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -2.65 (0.27), residues: 787
  helix: -1.16 (0.26), residues: 346
  sheet: -2.82 (1.15), residues: 22
  loop : -2.25 (0.26), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP A 473 
 HIS   0.014   0.002   HIS A 241 
 PHE   0.020   0.003   PHE A 327 
 TYR   0.023   0.002   TYR E 495 
 ARG   0.004   0.001   ARG E 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10121 (  211)
  hydrogen bonds       : angle       5.36952 (  597)
  SS BOND              : bond        0.00430 (    7)
  SS BOND              : angle       0.90077 (   14)
  covalent geometry    : bond        0.00713 ( 6592)
  covalent geometry    : angle       0.72735 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 78
  time to evaluate  : 0.682 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5784 (tm-30)
REVERT: A   42 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7553 (mm-40)
REVERT: A   75 GLU cc_start: 0.7440 (tp30) cc_final: 0.7238 (tp30)
REVERT: A  123 MET cc_start: 0.8166 (mtt) cc_final: 0.7909 (mtm)
REVERT: A  345 HIS cc_start: 0.1889 (OUTLIER) cc_final: 0.1395 (t70)
REVERT: A  360 MET cc_start: 0.2988 (tpt) cc_final: 0.0775 (ptm)
REVERT: A  378 HIS cc_start: 0.8817 (OUTLIER) cc_final: 0.8551 (m-70)
REVERT: E  439 ASN cc_start: 0.8500 (t0) cc_final: 0.8253 (t0)
  outliers start: 31
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1896
  time to fit residues: 26.8186
Evaluate side-chains
  91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  494 SER
Chi-restraints excluded: chain E residue  511 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0980
   chunk 36 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 524 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.182963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.144675 restraints weight = 7856.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.62
r_work: 0.3495 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.6546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6599  Z= 0.128
  Angle     :  0.522   5.621   8972  Z= 0.283
  Chirality :  0.042   0.184    934
  Planarity :  0.005   0.055   1165
  Dihedral  :  4.914  49.975    863
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.74 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -1.95 (0.29), residues: 787
  helix: -0.49 (0.29), residues: 339
  sheet: -2.88 (0.76), residues: 43
  loop : -1.81 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 473 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.014   0.001   PHE A 327 
 TYR   0.010   0.001   TYR E 495 
 ARG   0.004   0.000   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05950 (  211)
  hydrogen bonds       : angle       4.63614 (  597)
  SS BOND              : bond        0.00205 (    7)
  SS BOND              : angle       0.52375 (   14)
  covalent geometry    : bond        0.00271 ( 6592)
  covalent geometry    : angle       0.52219 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5839 (pt0)
REVERT: A   75 GLU cc_start: 0.7397 (tp30) cc_final: 0.7182 (tp30)
REVERT: A  345 HIS cc_start: 0.1618 (OUTLIER) cc_final: 0.1088 (t70)
REVERT: A  360 MET cc_start: 0.2658 (tpt) cc_final: 0.0905 (ptm)
REVERT: E  439 ASN cc_start: 0.8387 (t0) cc_final: 0.8108 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 96
  average time/residue: 0.1726
  time to fit residues: 22.7940
Evaluate side-chains
  87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  494 SER
Chi-restraints excluded: chain E residue  511 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.176797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.138532 restraints weight = 7724.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.61
r_work: 0.3426 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.7117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6599  Z= 0.165
  Angle     :  0.579   6.275   8972  Z= 0.312
  Chirality :  0.044   0.191    934
  Planarity :  0.005   0.053   1165
  Dihedral  :  4.978  47.963    863
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.74 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -1.93 (0.28), residues: 787
  helix: -0.45 (0.28), residues: 334
  sheet: -2.40 (0.76), residues: 46
  loop : -1.87 (0.28), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 473 
 HIS   0.010   0.001   HIS A 241 
 PHE   0.014   0.002   PHE A 230 
 TYR   0.015   0.002   TYR E 495 
 ARG   0.008   0.001   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07853 (  211)
  hydrogen bonds       : angle       4.74090 (  597)
  SS BOND              : bond        0.00274 (    7)
  SS BOND              : angle       0.62066 (   14)
  covalent geometry    : bond        0.00369 ( 6592)
  covalent geometry    : angle       0.57902 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5862 (tt0)
REVERT: A   42 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7416 (mm-40)
REVERT: A  345 HIS cc_start: 0.1208 (OUTLIER) cc_final: 0.0794 (t70)
REVERT: A  360 MET cc_start: 0.3026 (tpt) cc_final: 0.1670 (ptm)
REVERT: E  439 ASN cc_start: 0.8457 (t0) cc_final: 0.8229 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 97
  average time/residue: 0.1679
  time to fit residues: 22.4263
Evaluate side-chains
  85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  511 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.0060
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.3602

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.173558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.135800 restraints weight = 7806.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.66
r_work: 0.3393 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.7756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6599  Z= 0.179
  Angle     :  0.600   6.244   8972  Z= 0.322
  Chirality :  0.045   0.172    934
  Planarity :  0.005   0.053   1165
  Dihedral  :  5.041  45.327    863
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.45 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -1.93 (0.28), residues: 787
  helix: -0.41 (0.29), residues: 332
  sheet: -1.92 (0.79), residues: 44
  loop : -1.97 (0.27), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 473 
 HIS   0.008   0.001   HIS A 241 
 PHE   0.019   0.002   PHE A 369 
 TYR   0.015   0.001   TYR E 495 
 ARG   0.008   0.001   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07227 (  211)
  hydrogen bonds       : angle       4.67150 (  597)
  SS BOND              : bond        0.00230 (    7)
  SS BOND              : angle       0.55163 (   14)
  covalent geometry    : bond        0.00415 ( 6592)
  covalent geometry    : angle       0.60047 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5981 (tt0)
REVERT: A   42 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7362 (mm-40)
REVERT: A  243 TYR cc_start: 0.8055 (t80) cc_final: 0.7843 (t80)
REVERT: A  345 HIS cc_start: 0.1680 (OUTLIER) cc_final: 0.1139 (t70)
REVERT: A  360 MET cc_start: 0.3276 (tpt) cc_final: 0.2746 (ptm)
REVERT: A  470 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7654 (mmtp)
REVERT: A  531 GLN cc_start: 0.7405 (tp40) cc_final: 0.6602 (tt0)
REVERT: E  408 ARG cc_start: 0.7533 (ptp-170) cc_final: 0.6970 (ptt90)
REVERT: E  439 ASN cc_start: 0.8481 (t0) cc_final: 0.8249 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1818
  time to fit residues: 23.2519
Evaluate side-chains
  89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  494 SER
Chi-restraints excluded: chain E residue  511 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 8 optimal weight:    0.2980
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
E 460 ASN
** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.173383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.135805 restraints weight = 7783.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.65
r_work: 0.3393 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.7973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6599  Z= 0.149
  Angle     :  0.557   8.844   8972  Z= 0.296
  Chirality :  0.043   0.176    934
  Planarity :  0.005   0.049   1165
  Dihedral  :  4.395  16.965    861
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.03 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -1.68 (0.29), residues: 787
  helix: -0.10 (0.29), residues: 333
  sheet: -1.80 (0.78), residues: 44
  loop : -1.95 (0.27), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 473 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.022   0.001   PHE A 369 
 TYR   0.015   0.001   TYR A  50 
 ARG   0.007   0.000   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06622 (  211)
  hydrogen bonds       : angle       4.42060 (  597)
  SS BOND              : bond        0.00252 (    7)
  SS BOND              : angle       0.75770 (   14)
  covalent geometry    : bond        0.00336 ( 6592)
  covalent geometry    : angle       0.55629 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5880 (tt0)
REVERT: A   42 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7325 (mm-40)
REVERT: A  297 MET cc_start: -0.1479 (ptp) cc_final: -0.3365 (mmm)
REVERT: A  360 MET cc_start: 0.3427 (tpt) cc_final: 0.2836 (ptm)
REVERT: A  470 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7736 (mmtp)
REVERT: A  531 GLN cc_start: 0.7349 (tp-100) cc_final: 0.6413 (tt0)
REVERT: E  439 ASN cc_start: 0.8630 (t0) cc_final: 0.8383 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 90
  average time/residue: 0.1606
  time to fit residues: 20.4127
Evaluate side-chains
  87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  494 SER
Chi-restraints excluded: chain E residue  511 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 11 optimal weight:    0.3980
   chunk 69 optimal weight:    0.5980
   chunk 52 optimal weight:    0.1980
   chunk 76 optimal weight:    0.9990
   chunk 49 optimal weight:    0.4980
   chunk 73 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0570
   chunk 71 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.3498

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

Flipped N/Q/H residues before XYZ refinement:
** E 487 ASN ** 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 = 0.3998 r_free = 0.3998 target = 0.178556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.144747 restraints weight = 7760.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.52
r_work: 0.3475 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.7978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6599  Z= 0.107
  Angle     :  0.495   9.545   8972  Z= 0.261
  Chirality :  0.041   0.152    934
  Planarity :  0.004   0.044   1165
  Dihedral  :  4.000  17.315    861
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.45 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -1.21 (0.30), residues: 787
  helix:  0.39 (0.31), residues: 332
  sheet: -1.49 (1.06), residues: 30
  loop : -1.79 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 566 
 HIS   0.007   0.001   HIS A 345 
 PHE   0.011   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A  50 
 ARG   0.007   0.000   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04599 (  211)
  hydrogen bonds       : angle       4.12543 (  597)
  SS BOND              : bond        0.00089 (    7)
  SS BOND              : angle       0.84321 (   14)
  covalent geometry    : bond        0.00222 ( 6592)
  covalent geometry    : angle       0.49390 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5719 (tt0)
REVERT: A  297 MET cc_start: -0.1751 (ptp) cc_final: -0.2875 (mmm)
REVERT: A  360 MET cc_start: 0.3504 (tpt) cc_final: 0.3057 (ptm)
REVERT: A  364 VAL cc_start: 0.2139 (OUTLIER) cc_final: 0.1879 (t)
REVERT: A  470 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7756 (mmtp)
REVERT: A  531 GLN cc_start: 0.7233 (tp-100) cc_final: 0.6328 (tt0)
REVERT: A  548 THR cc_start: 0.7018 (OUTLIER) cc_final: 0.6723 (m)
REVERT: A  603 PHE cc_start: 0.7100 (t80) cc_final: 0.6887 (t80)
REVERT: E  439 ASN cc_start: 0.8537 (t0) cc_final: 0.8306 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 91
  average time/residue: 0.1717
  time to fit residues: 21.7004
Evaluate side-chains
  91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  494 SER
Chi-restraints excluded: chain E residue  511 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.0070
   chunk 74 optimal weight:    0.0980
   chunk 55 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
** E 487 ASN ** 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 = 0.3961 r_free = 0.3961 target = 0.173715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.136116 restraints weight = 7825.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.63
r_work: 0.3415 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.8201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6599  Z= 0.130
  Angle     :  0.536   9.564   8972  Z= 0.282
  Chirality :  0.042   0.167    934
  Planarity :  0.004   0.045   1165
  Dihedral  :  4.083  17.235    861
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.74 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -1.30 (0.29), residues: 787
  helix:  0.28 (0.30), residues: 336
  sheet: -1.57 (0.94), residues: 34
  loop : -1.81 (0.27), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 473 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.020   0.001   PHE A 369 
 TYR   0.012   0.001   TYR A  50 
 ARG   0.007   0.000   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05991 (  211)
  hydrogen bonds       : angle       4.21693 (  597)
  SS BOND              : bond        0.00282 (    7)
  SS BOND              : angle       0.77261 (   14)
  covalent geometry    : bond        0.00284 ( 6592)
  covalent geometry    : angle       0.53527 ( 8958)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
REVERT: A  297 MET cc_start: -0.1814 (ptp) cc_final: -0.2795 (mmm)
REVERT: A  360 MET cc_start: 0.3785 (tpt) cc_final: 0.3581 (ptm)
REVERT: A  470 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7585 (mmtp)
REVERT: A  531 GLN cc_start: 0.7293 (tp-100) cc_final: 0.6378 (tt0)
REVERT: A  548 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.7218 (m)
REVERT: A  603 PHE cc_start: 0.7205 (t80) cc_final: 0.6986 (t80)
REVERT: E  408 ARG cc_start: 0.7562 (ptp-170) cc_final: 0.6960 (ptt90)
REVERT: E  439 ASN cc_start: 0.8557 (t0) cc_final: 0.8344 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 94
  average time/residue: 0.1751
  time to fit residues: 22.7160
Evaluate side-chains
  88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  494 SER
Chi-restraints excluded: chain E residue  511 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
E 394 ASN
** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.176811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.139896 restraints weight = 7868.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.58
r_work: 0.3438 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.8302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6599  Z= 0.118
  Angle     :  0.514   9.150   8972  Z= 0.269
  Chirality :  0.041   0.152    934
  Planarity :  0.004   0.045   1165
  Dihedral  :  4.024  16.548    861
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 20.46 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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: -1.11 (0.29), residues: 787
  helix:  0.45 (0.30), residues: 335
  sheet: -1.31 (1.05), residues: 30
  loop : -1.74 (0.27), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 473 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.015   0.001   PHE A 369 
 TYR   0.010   0.001   TYR E 423 
 ARG   0.008   0.000   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05179 (  211)
  hydrogen bonds       : angle       4.05118 (  597)
  SS BOND              : bond        0.00140 (    7)
  SS BOND              : angle       0.73760 (   14)
  covalent geometry    : bond        0.00258 ( 6592)
  covalent geometry    : angle       0.51332 ( 8958)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3250.81 seconds
wall clock time: 57 minutes 1.87 seconds (3421.87 seconds total)