Starting phenix.real_space_refine
on Fri May  9 23:02:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j8b_61226/05_2025/9j8b_61226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j8b_61226/05_2025/9j8b_61226.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j8b_61226/05_2025/9j8b_61226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j8b_61226/05_2025/9j8b_61226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j8b_61226/05_2025/9j8b_61226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j8b_61226/05_2025/9j8b_61226.cif"
  }
  resolution = 3.9
  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
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=   0.026
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      34      5.16       5
     C    2774      2.51       5
     N     652      2.21       5
     O     698      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4158
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 4158
          Classifications: {'peptide': 524}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 24, 'TRANS': 499}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 3.13, per 1000 atoms: 0.75
  Number of scatterers: 4158
  At special positions: 0
  Unit cell: (76.5, 68.85, 93.5, 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      34     16.00
     O     698      8.00
     N     652      7.00
     C    2774      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 166 " - pdb=" SG  CYS A 175 " 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: 1.04
  Conformation dependent library (CDL) restraints added in 509.7 milliseconds
  

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  956

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      71.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 3.599A  pdb=" N   VAL A  69 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 79
      removed outlier: 4.128A  pdb=" N   TYR A  74 " --> pdb=" O   TRP A  70 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TYR A  77 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
    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 84 through 96
    Processing helix  chain 'A' and resid 97 through 99
      No H-bonds generated for 'chain 'A' and resid 97 through 99'
    Processing helix  chain 'A' and resid 100 through 110
      removed outlier: 4.004A  pdb=" N   ALA A 110 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 124
    Processing helix  chain 'A' and resid 125 through 139
      removed outlier: 3.521A  pdb=" N   TYR A 129 " --> pdb=" O   LYS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 154
      removed outlier: 3.609A  pdb=" N   VAL A 145 " --> pdb=" O   TYR A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 165
      removed outlier: 4.176A  pdb=" N   TYR A 165 " --> pdb=" O   PRO A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.959A  pdb=" N   TRP A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 211 through 216'
    Processing helix  chain 'A' and resid 233 through 254
      removed outlier: 3.730A  pdb=" N   VAL A 242 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   VAL A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   PHE A 248 " --> pdb=" O   TRP A 244 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   GLY A 254 " --> pdb=" O   CYS A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 279
      removed outlier: 3.796A  pdb=" N   VAL A 271 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG A 279 " --> pdb=" O   ILE A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 292
    Processing helix  chain 'A' and resid 299 through 303
      removed outlier: 4.058A  pdb=" N   LEU A 302 " --> pdb=" O   ASP A 299 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLU A 303 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 299 through 303'
    Processing helix  chain 'A' and resid 304 through 317
    Processing helix  chain 'A' and resid 326 through 332
    Processing helix  chain 'A' and resid 337 through 372
      removed outlier: 3.574A  pdb=" N   SER A 346 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A 347 " --> pdb=" O   VAL A 343 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ILE A 363 " --> pdb=" O   VAL A 359 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A 364 " --> pdb=" O   ILE A 360 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY A 365 " --> pdb=" O   PHE A 361 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE A 366 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 378
    Processing helix  chain 'A' and resid 385 through 397
      Proline residue:  A 391  - end of helix
    Processing helix  chain 'A' and resid 399 through 435
      removed outlier: 3.792A  pdb=" N   TRP A 403 " --> pdb=" O   ILE A 399 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   CYS A 421 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU A 426 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL A 434 " --> pdb=" O   ILE A 430 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLY A 435 " --> pdb=" O   VAL A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 458
      removed outlier: 3.878A  pdb=" N   VAL A 446 " --> pdb=" O   LYS A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 476
      removed outlier: 3.799A  pdb=" N   ASP A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASN A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR A 476 " --> pdb=" O   LEU A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 496
      removed outlier: 3.523A  pdb=" N   ILE A 496 " --> pdb=" O   ALA A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 510
      removed outlier: 3.963A  pdb=" N   TYR A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 506 " --> pdb=" O   TYR A 502 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLN A 507 " --> pdb=" O   PHE A 503 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   MET A 508 " --> pdb=" O   GLN A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 524
    Processing helix  chain 'A' and resid 524 through 540
      removed outlier: 3.534A  pdb=" N   VAL A 538 " --> pdb=" O   LEU A 534 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN A 540 " --> pdb=" O   PHE A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 547
    Processing helix  chain 'A' and resid 552 through 581
      removed outlier: 3.678A  pdb=" N   SER A 566 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL A 567 " --> pdb=" O   ALA A 563 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   CYS A 569 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   ILE A 570 " --> pdb=" O   SER A 566 " (cutoff:3.500A)
      Proline residue:  A 571  - end of helix
      removed outlier: 3.743A  pdb=" N   ARG A 580 " --> pdb=" O   PHE A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 595
      removed outlier: 3.816A  pdb=" N   LYS A 591 " --> pdb=" O   LEU A 587 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LYS A 595 " --> pdb=" O   LYS A 591 " (cutoff:3.500A)

    213 hydrogen bonds defined for protein.
    609 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: 0.99

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1232
        1.34 -     1.46: 1155
        1.46 -     1.58: 1852
        1.58 -     1.69: 0
        1.69 -     1.81: 52
  Bond restraints: 4291
  Sorted by residual:
  bond pdb=" N   GLY A  81 "
       pdb=" CA  GLY A  81 "
    ideal  model  delta    sigma   weight residual
    1.460  1.450  0.011 1.26e-02 6.30e+03 7.41e-01
  bond pdb=" CB  LYS A 333 "
       pdb=" CG  LYS A 333 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.90e-01
  bond pdb=" CA  GLY A  81 "
       pdb=" C   GLY A  81 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.011 1.33e-02 5.65e+03 6.84e-01
  bond pdb=" C   GLN A 542 "
       pdb=" N   PRO A 543 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.76e-01
  bond pdb=" C   VAL A 281 "
       pdb=" O   VAL A 281 "
    ideal  model  delta    sigma   weight residual
    1.233  1.241 -0.008 1.02e-02 9.61e+03 6.37e-01
  ... (remaining 4286 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 5582
        1.29 -     2.58: 207
        2.58 -     3.87: 37
        3.87 -     5.16: 21
        5.16 -     6.45: 6
  Bond angle restraints: 5853
  Sorted by residual:
  angle pdb=" N   LEU A 385 "
        pdb=" CA  LEU A 385 "
        pdb=" C   LEU A 385 "
      ideal   model   delta    sigma   weight residual
     114.04  109.15    4.89 1.24e+00 6.50e-01 1.56e+01
  angle pdb=" N   ILE A 496 "
        pdb=" CA  ILE A 496 "
        pdb=" C   ILE A 496 "
      ideal   model   delta    sigma   weight residual
     111.62  108.59    3.03 7.90e-01 1.60e+00 1.47e+01
  angle pdb=" N   ILE A 290 "
        pdb=" CA  ILE A 290 "
        pdb=" C   ILE A 290 "
      ideal   model   delta    sigma   weight residual
     111.81  108.79    3.02 8.60e-01 1.35e+00 1.24e+01
  angle pdb=" N   HIS A 607 "
        pdb=" CA  HIS A 607 "
        pdb=" C   HIS A 607 "
      ideal   model   delta    sigma   weight residual
     114.31  110.44    3.87 1.29e+00 6.01e-01 8.99e+00
  angle pdb=" N   GLU A 606 "
        pdb=" CA  GLU A 606 "
        pdb=" CB  GLU A 606 "
      ideal   model   delta    sigma   weight residual
     113.65  109.53    4.12 1.47e+00 4.63e-01 7.86e+00
  ... (remaining 5848 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2189
       17.95 -    35.89: 180
       35.89 -    53.84: 38
       53.84 -    71.79: 3
       71.79 -    89.73: 8
  Dihedral angle restraints: 2418
    sinusoidal: 908
      harmonic: 1510
  Sorted by residual:
  dihedral pdb=" CB  CYS A 166 "
           pdb=" SG  CYS A 166 "
           pdb=" SG  CYS A 175 "
           pdb=" CB  CYS A 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.96   85.96     1      1.00e+01 1.00e-02 8.92e+01
  dihedral pdb=" CA  TYR A 541 "
           pdb=" C   TYR A 541 "
           pdb=" N   GLN A 542 "
           pdb=" CA  GLN A 542 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.95   18.05     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  GLU A 213 "
           pdb=" C   GLU A 213 "
           pdb=" N   TYR A 214 "
           pdb=" CA  TYR A 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.43   16.57     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 2415 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 465
       0.037 -    0.073: 142
       0.073 -    0.110: 29
       0.110 -    0.146: 10
       0.146 -    0.183: 1
  Chirality restraints: 647
  Sorted by residual:
  chirality pdb=" CA  THR A 295 "
            pdb=" N   THR A 295 "
            pdb=" C   THR A 295 "
            pdb=" CB  THR A 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.34e-01
  chirality pdb=" CA  SER A 526 "
            pdb=" N   SER A 526 "
            pdb=" C   SER A 526 "
            pdb=" CB  SER A 526 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CB  THR A 295 "
            pdb=" CA  THR A 295 "
            pdb=" OG1 THR A 295 "
            pdb=" CG2 THR A 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 644 not shown)

  Planarity restraints: 719
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 358 "    0.012 2.00e-02 2.50e+03   1.28e-02 2.86e+00
        pdb=" CG  PHE A 358 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 358 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 358 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 358 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 358 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 358 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 551 "   -0.027 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO A 552 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 552 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 552 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 513 "    0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO A 514 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 514 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 514 "    0.021 5.00e-02 4.00e+02
  ... (remaining 716 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 560
        2.76 -     3.29: 4250
        3.29 -     3.83: 6575
        3.83 -     4.36: 7334
        4.36 -     4.90: 12671
  Nonbonded interactions: 31390
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 475 "
            pdb=" OG  SER A 479 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG1 THR A 208 "
            pdb=" OE2 GLU A 213 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   PRO A  98 "
            pdb=" NE1 TRP A 522 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OH  TYR A 142 "
            pdb=" OH  TYR A 316 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   ALA A 266 "
            pdb=" OG1 THR A 267 "
     model   vdw
     2.315 3.040
  ... (remaining 31385 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 group one per residue
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:             0.830
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.040
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
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      :  0.003   0.033   4292  Z= 0.130
  Angle     :  0.644   6.455   5855  Z= 0.355
  Chirality :  0.039   0.183    647
  Planarity :  0.004   0.040    719
  Dihedral  : 14.285  89.735   1459
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.40), residues: 518
  helix:  0.98 (0.31), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.55 (0.46), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 522 
 HIS   0.009   0.001   HIS A 548 
 PHE   0.030   0.001   PHE A 358 
 TYR   0.018   0.001   TYR A 549 
 ARG   0.002   0.000   ARG A 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21611 (  213)
  hydrogen bonds       : angle       6.37730 (  609)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       1.91044 (    2)
  covalent geometry    : bond        0.00264 ( 4291)
  covalent geometry    : angle       0.64283 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 ASP cc_start: 0.8330 (m-30) cc_final: 0.8113 (m-30)
REVERT: A  212 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7157 (mp0)
REVERT: A  424 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8011 (tm-30)
REVERT: A  428 THR cc_start: 0.8704 (m) cc_final: 0.8417 (m)
REVERT: A  430 ILE cc_start: 0.8152 (tt) cc_final: 0.7832 (tp)
REVERT: A  457 LEU cc_start: 0.8434 (tp) cc_final: 0.8220 (tp)
REVERT: A  507 GLN cc_start: 0.8617 (mm110) cc_final: 0.8240 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1524
  time to fit residues: 25.2938
Evaluate side-chains
  106 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0060
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    1.0798

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN
A 540 GLN
A 548 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.142110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.116755 restraints weight = 6751.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.119925 restraints weight = 4013.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.122149 restraints weight = 2904.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4292  Z= 0.156
  Angle     :  0.625   6.414   5855  Z= 0.317
  Chirality :  0.042   0.221    647
  Planarity :  0.005   0.039    719
  Dihedral  :  3.884  19.558    572
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.76 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.39), residues: 518
  helix:  0.84 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.34 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 170 
 HIS   0.006   0.001   HIS A 548 
 PHE   0.020   0.002   PHE A 248 
 TYR   0.024   0.002   TYR A 549 
 ARG   0.004   0.001   ARG A 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04547 (  213)
  hydrogen bonds       : angle       4.36020 (  609)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       1.50133 (    2)
  covalent geometry    : bond        0.00361 ( 4291)
  covalent geometry    : angle       0.62463 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A  424 GLU cc_start: 0.8594 (tm-30) cc_final: 0.7948 (tm-30)
REVERT: A  428 THR cc_start: 0.8815 (m) cc_final: 0.8390 (m)
REVERT: A  430 ILE cc_start: 0.8146 (tt) cc_final: 0.7857 (tp)
  outliers start: 11
  outliers final: 5
  residues processed: 125
  average time/residue: 0.1268
  time to fit residues: 20.9278
Evaluate side-chains
  112 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  526 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.139238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.113678 restraints weight = 6679.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.116880 restraints weight = 3979.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.118963 restraints weight = 2852.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4292  Z= 0.135
  Angle     :  0.587   7.341   5855  Z= 0.296
  Chirality :  0.039   0.134    647
  Planarity :  0.004   0.038    719
  Dihedral  :  3.845  19.883    572
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.77 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.39), residues: 518
  helix:  1.04 (0.30), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.31 (0.51), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 499 
 PHE   0.016   0.001   PHE A 531 
 TYR   0.022   0.001   TYR A 549 
 ARG   0.006   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04113 (  213)
  hydrogen bonds       : angle       4.14698 (  609)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       1.04551 (    2)
  covalent geometry    : bond        0.00315 ( 4291)
  covalent geometry    : angle       0.58633 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  402 LEU cc_start: 0.7969 (tp) cc_final: 0.7592 (tp)
REVERT: A  419 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8195 (mt0)
REVERT: A  424 GLU cc_start: 0.8620 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: A  428 THR cc_start: 0.8791 (m) cc_final: 0.8526 (m)
REVERT: A  430 ILE cc_start: 0.8154 (tt) cc_final: 0.7846 (tp)
  outliers start: 13
  outliers final: 5
  residues processed: 118
  average time/residue: 0.1288
  time to fit residues: 20.0576
Evaluate side-chains
  114 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  419 GLN
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  537 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 31 optimal weight:    0.2980
   chunk 49 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 24 optimal weight:    0.0370
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0070
   chunk 5 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.2276

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.143156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.117544 restraints weight = 6630.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.120969 restraints weight = 3929.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.123191 restraints weight = 2793.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4292  Z= 0.116
  Angle     :  0.591   8.361   5855  Z= 0.292
  Chirality :  0.041   0.317    647
  Planarity :  0.004   0.035    719
  Dihedral  :  3.739  21.066    572
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 19.59 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.40), residues: 518
  helix:  1.14 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.12 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 381 
 PHE   0.025   0.001   PHE A 366 
 TYR   0.016   0.001   TYR A 549 
 ARG   0.006   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  213)
  hydrogen bonds       : angle       3.95183 (  609)
  SS BOND              : bond        0.00010 (    1)
  SS BOND              : angle       0.97414 (    2)
  covalent geometry    : bond        0.00254 ( 4291)
  covalent geometry    : angle       0.59063 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  424 GLU cc_start: 0.8545 (tm-30) cc_final: 0.7988 (tm-30)
REVERT: A  428 THR cc_start: 0.8787 (m) cc_final: 0.8341 (m)
REVERT: A  430 ILE cc_start: 0.8091 (tt) cc_final: 0.7795 (tp)
REVERT: A  598 ARG cc_start: 0.8120 (mmt180) cc_final: 0.7870 (mmm-85)
  outliers start: 8
  outliers final: 3
  residues processed: 115
  average time/residue: 0.1397
  time to fit residues: 20.6068
Evaluate side-chains
  108 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  526 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 37 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 143 ASN
A 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.145521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.120346 restraints weight = 6943.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.123650 restraints weight = 4133.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.125947 restraints weight = 2949.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4292  Z= 0.125
  Angle     :  0.589   8.362   5855  Z= 0.293
  Chirality :  0.039   0.149    647
  Planarity :  0.004   0.035    719
  Dihedral  :  3.731  21.680    572
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.73 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.40), residues: 518
  helix:  1.19 (0.30), residues: 342
  sheet:  None (None), residues: 0
  loop : -1.04 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 607 
 PHE   0.018   0.001   PHE A 531 
 TYR   0.018   0.001   TYR A 549 
 ARG   0.009   0.001   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  213)
  hydrogen bonds       : angle       3.86426 (  609)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.94872 (    2)
  covalent geometry    : bond        0.00290 ( 4291)
  covalent geometry    : angle       0.58859 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A  143 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8289 (m-40)
REVERT: A  424 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7977 (tm-30)
REVERT: A  428 THR cc_start: 0.8814 (m) cc_final: 0.8324 (m)
REVERT: A  430 ILE cc_start: 0.8082 (tt) cc_final: 0.7764 (tp)
REVERT: A  598 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7830 (mmm-85)
  outliers start: 10
  outliers final: 6
  residues processed: 111
  average time/residue: 0.1221
  time to fit residues: 18.0106
Evaluate side-chains
  110 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  143 ASN
Chi-restraints excluded: chain A residue  419 GLN
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  537 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 51 optimal weight:    0.1980
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 11 optimal weight:    0.1980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN
** A 592 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 = 0.3534 r_free = 0.3534 target = 0.139654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.113865 restraints weight = 6649.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.117086 restraints weight = 4002.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.119455 restraints weight = 2869.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4292  Z= 0.129
  Angle     :  0.593   8.030   5855  Z= 0.295
  Chirality :  0.041   0.254    647
  Planarity :  0.004   0.034    719
  Dihedral  :  3.713  21.920    572
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 21.41 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.40), residues: 518
  helix:  1.27 (0.30), residues: 341
  sheet:  None (None), residues: 0
  loop : -1.12 (0.51), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 499 
 PHE   0.018   0.001   PHE A 531 
 TYR   0.013   0.001   TYR A 549 
 ARG   0.007   0.001   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03607 (  213)
  hydrogen bonds       : angle       3.85822 (  609)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.83887 (    2)
  covalent geometry    : bond        0.00302 ( 4291)
  covalent geometry    : angle       0.59335 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  424 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: A  428 THR cc_start: 0.8820 (m) cc_final: 0.8333 (m)
REVERT: A  430 ILE cc_start: 0.8086 (tt) cc_final: 0.7766 (tp)
REVERT: A  598 ARG cc_start: 0.8202 (mmt180) cc_final: 0.7877 (mmm-85)
  outliers start: 12
  outliers final: 8
  residues processed: 114
  average time/residue: 0.1204
  time to fit residues: 18.2126
Evaluate side-chains
  111 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  419 GLN
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  537 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 143 ASN
A 313 GLN
A 419 GLN
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.138758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.112974 restraints weight = 6760.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.116309 restraints weight = 4002.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.118666 restraints weight = 2843.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4292  Z= 0.142
  Angle     :  0.604   8.046   5855  Z= 0.304
  Chirality :  0.040   0.141    647
  Planarity :  0.004   0.036    719
  Dihedral  :  3.756  21.677    572
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.55 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.40), residues: 518
  helix:  1.27 (0.30), residues: 341
  sheet:  None (None), residues: 0
  loop : -1.12 (0.51), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 370 
 PHE   0.021   0.001   PHE A 101 
 TYR   0.024   0.001   TYR A 549 
 ARG   0.008   0.001   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03727 (  213)
  hydrogen bonds       : angle       3.87425 (  609)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       0.89119 (    2)
  covalent geometry    : bond        0.00333 ( 4291)
  covalent geometry    : angle       0.60371 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A  424 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: A  428 THR cc_start: 0.8837 (m) cc_final: 0.8634 (m)
REVERT: A  430 ILE cc_start: 0.8137 (tt) cc_final: 0.7833 (tp)
REVERT: A  588 GLN cc_start: 0.8165 (tp40) cc_final: 0.7381 (tp-100)
REVERT: A  598 ARG cc_start: 0.8211 (mmt180) cc_final: 0.7899 (mmm-85)
  outliers start: 11
  outliers final: 7
  residues processed: 108
  average time/residue: 0.1240
  time to fit residues: 17.7866
Evaluate side-chains
  108 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  537 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 14 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0070
   chunk 23 optimal weight:    0.0470
   chunk 28 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.3694

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN
A 592 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.142035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.116042 restraints weight = 6515.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.119394 restraints weight = 3924.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.121704 restraints weight = 2818.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4292  Z= 0.111
  Angle     :  0.587   7.500   5855  Z= 0.289
  Chirality :  0.041   0.324    647
  Planarity :  0.004   0.033    719
  Dihedral  :  3.672  21.752    572
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 23.23 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.40), residues: 518
  helix:  1.33 (0.30), residues: 341
  sheet:  None (None), residues: 0
  loop : -1.04 (0.51), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 170 
 HIS   0.002   0.001   HIS A 548 
 PHE   0.021   0.001   PHE A 101 
 TYR   0.015   0.001   TYR A 549 
 ARG   0.005   0.000   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03207 (  213)
  hydrogen bonds       : angle       3.75518 (  609)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.74039 (    2)
  covalent geometry    : bond        0.00246 ( 4291)
  covalent geometry    : angle       0.58739 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A  212 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7194 (mp0)
REVERT: A  328 MET cc_start: 0.6375 (mtt) cc_final: 0.5906 (mtt)
REVERT: A  424 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8126 (tm-30)
REVERT: A  430 ILE cc_start: 0.8071 (tt) cc_final: 0.7785 (tp)
REVERT: A  588 GLN cc_start: 0.8108 (tp40) cc_final: 0.7468 (tp-100)
REVERT: A  598 ARG cc_start: 0.8172 (mmt180) cc_final: 0.7815 (mmm-85)
  outliers start: 9
  outliers final: 3
  residues processed: 112
  average time/residue: 0.1254
  time to fit residues: 18.4632
Evaluate side-chains
  104 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  526 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0170
   chunk 24 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0270
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.139668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.114916 restraints weight = 6542.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.118235 restraints weight = 3819.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.120418 restraints weight = 2690.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4292  Z= 0.125
  Angle     :  0.603   8.232   5855  Z= 0.296
  Chirality :  0.040   0.188    647
  Planarity :  0.004   0.033    719
  Dihedral  :  3.670  21.388    572
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 23.69 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.40), residues: 518
  helix:  1.37 (0.30), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.07 (0.51), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 370 
 PHE   0.019   0.001   PHE A 531 
 TYR   0.015   0.001   TYR A 549 
 ARG   0.006   0.001   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03491 (  213)
  hydrogen bonds       : angle       3.81574 (  609)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.86927 (    2)
  covalent geometry    : bond        0.00292 ( 4291)
  covalent geometry    : angle       0.60325 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  328 MET cc_start: 0.6482 (mtt) cc_final: 0.6010 (mtt)
REVERT: A  424 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8071 (tm-30)
REVERT: A  430 ILE cc_start: 0.8116 (tt) cc_final: 0.7813 (tp)
REVERT: A  588 GLN cc_start: 0.8146 (tp40) cc_final: 0.7498 (tp-100)
REVERT: A  598 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7778 (mmm-85)
  outliers start: 6
  outliers final: 3
  residues processed: 102
  average time/residue: 0.1272
  time to fit residues: 17.3681
Evaluate side-chains
  101 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  526 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0270
   chunk 42 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.141123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.115195 restraints weight = 6607.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.118529 restraints weight = 3959.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.120763 restraints weight = 2832.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4292  Z= 0.115
  Angle     :  0.609  10.821   5855  Z= 0.296
  Chirality :  0.042   0.365    647
  Planarity :  0.004   0.033    719
  Dihedral  :  3.646  21.559    572
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 24.37 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.40), residues: 518
  helix:  1.35 (0.30), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.09 (0.50), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 170 
 HIS   0.013   0.001   HIS A 370 
 PHE   0.019   0.001   PHE A 101 
 TYR   0.013   0.001   TYR A 549 
 ARG   0.006   0.001   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  213)
  hydrogen bonds       : angle       3.78019 (  609)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.76551 (    2)
  covalent geometry    : bond        0.00262 ( 4291)
  covalent geometry    : angle       0.60897 ( 5853)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A  212 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7234 (mp0)
REVERT: A  328 MET cc_start: 0.6459 (mtt) cc_final: 0.6013 (mtt)
REVERT: A  424 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8117 (tm-30)
REVERT: A  430 ILE cc_start: 0.8056 (tt) cc_final: 0.7814 (tp)
REVERT: A  580 ARG cc_start: 0.7377 (mmt90) cc_final: 0.7145 (mpt-90)
REVERT: A  588 GLN cc_start: 0.8203 (tp40) cc_final: 0.7535 (tp-100)
REVERT: A  598 ARG cc_start: 0.8186 (mmt180) cc_final: 0.7835 (mmm-85)
  outliers start: 4
  outliers final: 3
  residues processed: 103
  average time/residue: 0.1264
  time to fit residues: 17.3703
Evaluate side-chains
  102 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  526 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0020
   chunk 41 optimal weight:    0.6980
   chunk 49 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.147864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.122953 restraints weight = 6594.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.126210 restraints weight = 3919.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.128648 restraints weight = 2794.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4292  Z= 0.113
  Angle     :  0.619  10.471   5855  Z= 0.297
  Chirality :  0.042   0.348    647
  Planarity :  0.004   0.034    719
  Dihedral  :  3.589  21.079    572
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 25.28 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.40), residues: 518
  helix:  1.40 (0.30), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.11 (0.49), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 170 
 HIS   0.012   0.001   HIS A 370 
 PHE   0.018   0.001   PHE A 531 
 TYR   0.009   0.001   TYR A  74 
 ARG   0.006   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  213)
  hydrogen bonds       : angle       3.73101 (  609)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.84106 (    2)
  covalent geometry    : bond        0.00254 ( 4291)
  covalent geometry    : angle       0.61858 ( 5853)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1618.68 seconds
wall clock time: 29 minutes 5.84 seconds (1745.84 seconds total)