Starting phenix.real_space_refine
on Wed Sep 17 04:28:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j8b_61226/09_2025/9j8b_61226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j8b_61226/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j8b_61226/09_2025/9j8b_61226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j8b_61226/09_2025/9j8b_61226.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j8b_61226/09_2025/9j8b_61226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j8b_61226/09_2025/9j8b_61226.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.38, per 1000 atoms: 0.33
  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: 0.36
  Conformation dependent library (CDL) restraints added in 164.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.12
  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: 0.71

  Time building geometry restraints manager: 0.51 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:             1.540
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.230
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.650
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 119 
 TYR   0.018   0.001   TYR A 549 
 PHE   0.030   0.001   PHE A 358 
 TRP   0.009   0.001   TRP A 522 
 HIS   0.009   0.001   HIS A 548 

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

*********************** 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  : 0.155 
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: 0.8222 (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: 0.0651
  time to fit residues: 11.0203
Evaluate side-chains
  105 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0270
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.6640

-------------------------------------------------------------------------------
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 548 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.141207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.115268 restraints weight = 6691.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.118586 restraints weight = 3941.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.120921 restraints weight = 2825.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.122384 restraints weight = 2263.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.123211 restraints weight = 1960.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1815

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= 0.134
  Angle     :  0.606   6.079   5855  Z= 0.306
  Chirality :  0.040   0.207    647
  Planarity :  0.004   0.037    719
  Dihedral  :  3.786  19.174    572
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.53 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.39), residues: 518
  helix:  0.91 (0.29), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.18 (0.51), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 580 
 TYR   0.022   0.002   TYR A 549 
 PHE   0.019   0.001   PHE A 248 
 TRP   0.019   0.001   TRP A 170 
 HIS   0.006   0.001   HIS A 548 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4291)
  covalent geometry    : angle       0.60513 ( 5853)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       1.50651 (    2)
  hydrogen bonds       : bond        0.04612 (  213)
  hydrogen bonds       : angle       4.35533 (  609)

*********************** 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
  130 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 PHE cc_start: 0.8550 (t80) cc_final: 0.8118 (t80)
REVERT: A  424 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7981 (tm-30)
REVERT: A  428 THR cc_start: 0.8790 (m) cc_final: 0.8292 (m)
REVERT: A  430 ILE cc_start: 0.8107 (tt) cc_final: 0.7819 (tp)
REVERT: A  570 ILE cc_start: 0.8892 (mt) cc_final: 0.8680 (mt)
  outliers start: 8
  outliers final: 3
  residues processed: 126
  average time/residue: 0.0557
  time to fit residues: 9.3667
Evaluate side-chains
  114 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue  493 ILE
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 17 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0980
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 499 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.143568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.118476 restraints weight = 6785.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.121786 restraints weight = 3970.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.123888 restraints weight = 2823.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.125541 restraints weight = 2279.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.126533 restraints weight = 1959.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2125

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= 0.123
  Angle     :  0.576   8.151   5855  Z= 0.288
  Chirality :  0.039   0.126    647
  Planarity :  0.004   0.036    719
  Dihedral  :  3.772  19.153    572
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.08 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.39), residues: 518
  helix:  0.98 (0.30), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.16 (0.50), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 580 
 TYR   0.022   0.001   TYR A 549 
 PHE   0.015   0.001   PHE A 531 
 TRP   0.021   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 548 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4291)
  covalent geometry    : angle       0.57625 ( 5853)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       1.07416 (    2)
  hydrogen bonds       : bond        0.03924 (  213)
  hydrogen bonds       : angle       4.09879 (  609)

*********************** 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
  124 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  424 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7964 (tm-30)
REVERT: A  428 THR cc_start: 0.8759 (m) cc_final: 0.8272 (m)
REVERT: A  430 ILE cc_start: 0.8107 (tt) cc_final: 0.7813 (tp)
  outliers start: 11
  outliers final: 6
  residues processed: 118
  average time/residue: 0.0624
  time to fit residues: 9.5818
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  : 0.166 
-------------------------------------------------------------------------------
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  467 ILE
Chi-restraints excluded: chain A residue  499 HIS
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 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 43 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0970
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 499 HIS ** 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 = 0.3622 r_free = 0.3622 target = 0.145611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120321 restraints weight = 6735.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.123622 restraints weight = 4034.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125911 restraints weight = 2901.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.127365 restraints weight = 2334.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.128402 restraints weight = 2026.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2395

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= 0.126
  Angle     :  0.582   6.058   5855  Z= 0.292
  Chirality :  0.040   0.271    647
  Planarity :  0.004   0.034    719
  Dihedral  :  3.722  18.856    572
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.13 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.39), residues: 518
  helix:  1.00 (0.30), residues: 344
  sheet:  None (None), residues: 0
  loop : -1.10 (0.51), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 523 
 TYR   0.020   0.001   TYR A 549 
 PHE   0.023   0.001   PHE A 366 
 TRP   0.022   0.001   TRP A 170 
 HIS   0.003   0.000   HIS A 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4291)
  covalent geometry    : angle       0.58213 ( 5853)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       0.98364 (    2)
  hydrogen bonds       : bond        0.03706 (  213)
  hydrogen bonds       : angle       3.98697 (  609)

*********************** 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
  123 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A  424 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8017 (tm-30)
REVERT: A  428 THR cc_start: 0.8798 (m) cc_final: 0.8332 (m)
REVERT: A  430 ILE cc_start: 0.8127 (tt) cc_final: 0.7819 (tp)
REVERT: A  598 ARG cc_start: 0.8080 (mmt180) cc_final: 0.7843 (mmm-85)
  outliers start: 10
  outliers final: 6
  residues processed: 117
  average time/residue: 0.0580
  time to fit residues: 8.8877
Evaluate side-chains
  112 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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  445 TYR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 51 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 499 HIS
** 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 = 0.3636 r_free = 0.3636 target = 0.146823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.121632 restraints weight = 6806.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.125033 restraints weight = 3969.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.127363 restraints weight = 2802.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.128562 restraints weight = 2230.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.129751 restraints weight = 1953.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2558

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= 0.123
  Angle     :  0.586   7.556   5855  Z= 0.288
  Chirality :  0.039   0.138    647
  Planarity :  0.004   0.036    719
  Dihedral  :  3.756  17.382    572
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.50 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.40), residues: 518
  helix:  1.15 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.09 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 580 
 TYR   0.021   0.001   TYR A 549 
 PHE   0.018   0.001   PHE A 366 
 TRP   0.022   0.001   TRP A 170 
 HIS   0.006   0.001   HIS A 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4291)
  covalent geometry    : angle       0.58597 ( 5853)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       0.94546 (    2)
  hydrogen bonds       : bond        0.03538 (  213)
  hydrogen bonds       : angle       3.87833 (  609)

*********************** 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
  121 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: A  424 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8192 (tm-30)
REVERT: A  428 THR cc_start: 0.8826 (m) cc_final: 0.8556 (m)
REVERT: A  430 ILE cc_start: 0.8133 (tt) cc_final: 0.7865 (tp)
REVERT: A  598 ARG cc_start: 0.8117 (mmt180) cc_final: 0.7814 (mmm-85)
  outliers start: 12
  outliers final: 7
  residues processed: 115
  average time/residue: 0.0576
  time to fit residues: 8.7856
Evaluate side-chains
  111 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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  445 TYR
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  535 VAL
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 19 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 12 optimal weight:    9.9990
   chunk 4 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 499 HIS
** 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 = 0.3598 r_free = 0.3598 target = 0.144046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.118291 restraints weight = 6864.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.121631 restraints weight = 4128.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.123712 restraints weight = 2970.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.125412 restraints weight = 2414.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.126166 restraints weight = 2082.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2766

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= 0.125
  Angle     :  0.604   6.914   5855  Z= 0.295
  Chirality :  0.041   0.264    647
  Planarity :  0.004   0.036    719
  Dihedral  :  3.751  17.487    572
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.40), residues: 518
  helix:  1.15 (0.30), residues: 344
  sheet:  None (None), residues: 0
  loop : -1.01 (0.51), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 580 
 TYR   0.012   0.001   TYR A 497 
 PHE   0.018   0.001   PHE A 531 
 TRP   0.023   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4291)
  covalent geometry    : angle       0.60355 ( 5853)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.82953 (    2)
  hydrogen bonds       : bond        0.03456 (  213)
  hydrogen bonds       : angle       3.84887 (  609)

*********************** 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  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  424 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: A  428 THR cc_start: 0.8814 (m) cc_final: 0.8547 (m)
REVERT: A  430 ILE cc_start: 0.8187 (tt) cc_final: 0.7891 (tp)
REVERT: A  598 ARG cc_start: 0.8167 (mmt180) cc_final: 0.7876 (mmm-85)
  outliers start: 12
  outliers final: 8
  residues processed: 113
  average time/residue: 0.0456
  time to fit residues: 7.0383
Evaluate side-chains
  113 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
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  283 LEU
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  535 VAL
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:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 23 optimal weight:    0.1980
   chunk 30 optimal weight:    0.2980
   chunk 46 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0970
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0030
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.1788

-------------------------------------------------------------------------------
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 499 HIS
A 592 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.149748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.124712 restraints weight = 6768.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.128213 restraints weight = 3923.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.130647 restraints weight = 2755.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.132109 restraints weight = 2174.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.133230 restraints weight = 1868.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2944

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= 0.114
  Angle     :  0.577   6.757   5855  Z= 0.288
  Chirality :  0.038   0.132    647
  Planarity :  0.004   0.035    719
  Dihedral  :  3.686  18.798    572
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 23.01 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.40), residues: 518
  helix:  1.26 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.05 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 580 
 TYR   0.020   0.001   TYR A 549 
 PHE   0.016   0.001   PHE A 531 
 TRP   0.026   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4291)
  covalent geometry    : angle       0.57667 ( 5853)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.80781 (    2)
  hydrogen bonds       : bond        0.03186 (  213)
  hydrogen bonds       : angle       3.73774 (  609)

*********************** 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
  115 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7087 (mp0)
REVERT: A  424 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8211 (tm-30)
REVERT: A  430 ILE cc_start: 0.8126 (tt) cc_final: 0.7829 (tp)
REVERT: A  598 ARG cc_start: 0.8132 (mmt180) cc_final: 0.7785 (mmm-85)
  outliers start: 7
  outliers final: 4
  residues processed: 111
  average time/residue: 0.0495
  time to fit residues: 7.4492
Evaluate side-chains
  111 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  526 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0470
   chunk 19 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.6878

-------------------------------------------------------------------------------
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
A 499 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.115269 restraints weight = 6724.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.118578 restraints weight = 4099.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.120736 restraints weight = 2983.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.122404 restraints weight = 2434.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.123337 restraints weight = 2109.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3044

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= 0.123
  Angle     :  0.595   7.738   5855  Z= 0.295
  Chirality :  0.041   0.317    647
  Planarity :  0.004   0.037    719
  Dihedral  :  3.675  20.275    572
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.40), residues: 518
  helix:  1.28 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.10 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 580 
 TYR   0.016   0.001   TYR A 549 
 PHE   0.025   0.001   PHE A 366 
 TRP   0.029   0.001   TRP A 170 
 HIS   0.003   0.000   HIS A 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4291)
  covalent geometry    : angle       0.59528 ( 5853)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.85204 (    2)
  hydrogen bonds       : bond        0.03280 (  213)
  hydrogen bonds       : angle       3.75086 (  609)

*********************** 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
  121 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  424 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8145 (tm-30)
REVERT: A  430 ILE cc_start: 0.8146 (tt) cc_final: 0.7846 (tp)
REVERT: A  588 GLN cc_start: 0.8092 (tp40) cc_final: 0.7465 (tp-100)
REVERT: A  598 ARG cc_start: 0.8124 (mmt180) cc_final: 0.7794 (mmm-85)
  outliers start: 11
  outliers final: 5
  residues processed: 115
  average time/residue: 0.0589
  time to fit residues: 8.9708
Evaluate side-chains
  113 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  499 HIS
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 9 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.142494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.116653 restraints weight = 6770.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.120047 restraints weight = 4051.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.122435 restraints weight = 2895.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.123890 restraints weight = 2311.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.124978 restraints weight = 2001.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3073

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= 0.129
  Angle     :  0.603   7.209   5855  Z= 0.300
  Chirality :  0.040   0.205    647
  Planarity :  0.004   0.035    719
  Dihedral  :  3.707  20.772    572
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 24.60 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.40), residues: 518
  helix:  1.28 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.10 (0.50), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 500 
 TYR   0.013   0.001   TYR A 549 
 PHE   0.034   0.002   PHE A 366 
 TRP   0.028   0.001   TRP A 170 
 HIS   0.006   0.001   HIS A 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4291)
  covalent geometry    : angle       0.60240 ( 5853)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       0.86157 (    2)
  hydrogen bonds       : bond        0.03382 (  213)
  hydrogen bonds       : angle       3.80538 (  609)

*********************** 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
  117 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7111 (mp0)
REVERT: A  424 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: A  430 ILE cc_start: 0.8118 (tt) cc_final: 0.7815 (tp)
REVERT: A  588 GLN cc_start: 0.8119 (tp40) cc_final: 0.7511 (tp-100)
REVERT: A  598 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7782 (mmm-85)
  outliers start: 8
  outliers final: 4
  residues processed: 112
  average time/residue: 0.0542
  time to fit residues: 8.2321
Evaluate side-chains
  111 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue  283 LEU
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 50 optimal weight:    4.9990
   chunk 38 optimal weight:    0.1980
   chunk 40 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 18 optimal weight:    0.4980
   chunk 8 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 28 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.149030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.124035 restraints weight = 6659.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.127390 restraints weight = 4034.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.129769 restraints weight = 2882.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.131213 restraints weight = 2292.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.132319 restraints weight = 1987.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4292  Z= 0.116
  Angle     :  0.611  10.857   5855  Z= 0.300
  Chirality :  0.041   0.371    647
  Planarity :  0.004   0.036    719
  Dihedral  :  3.673  21.462    572
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 25.28 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.40), residues: 518
  helix:  1.32 (0.30), residues: 344
  sheet:  None (None), residues: 0
  loop : -1.11 (0.50), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 580 
 TYR   0.012   0.001   TYR A 549 
 PHE   0.023   0.001   PHE A 101 
 TRP   0.029   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4291)
  covalent geometry    : angle       0.61115 ( 5853)
  SS BOND              : bond        0.00031 (    1)
  SS BOND              : angle       0.79515 (    2)
  hydrogen bonds       : bond        0.03128 (  213)
  hydrogen bonds       : angle       3.73152 (  609)

********************** 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
  110 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7103 (mp0)
REVERT: A  424 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: A  430 ILE cc_start: 0.8067 (tt) cc_final: 0.7772 (tp)
REVERT: A  588 GLN cc_start: 0.8144 (tp40) cc_final: 0.7532 (tp-100)
REVERT: A  598 ARG cc_start: 0.8151 (mmt180) cc_final: 0.7809 (mmm-85)
  outliers start: 4
  outliers final: 4
  residues processed: 108
  average time/residue: 0.0510
  time to fit residues: 7.4916
Evaluate side-chains
  108 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  283 LEU
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 42 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 30 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3589 r_free = 0.3589 target = 0.143157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.117139 restraints weight = 6769.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120528 restraints weight = 4076.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.122872 restraints weight = 2924.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.124315 restraints weight = 2346.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.125129 restraints weight = 2034.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3227

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= 0.125
  Angle     :  0.611  10.190   5855  Z= 0.299
  Chirality :  0.042   0.357    647
  Planarity :  0.004   0.035    719
  Dihedral  :  3.676  21.443    572
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 25.28 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.40), residues: 518
  helix:  1.35 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.13 (0.50), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 580 
 TYR   0.019   0.001   TYR A 549 
 PHE   0.021   0.001   PHE A 101 
 TRP   0.028   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4291)
  covalent geometry    : angle       0.61043 ( 5853)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.87776 (    2)
  hydrogen bonds       : bond        0.03310 (  213)
  hydrogen bonds       : angle       3.78257 (  609)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 860.79 seconds
wall clock time: 15 minutes 34.77 seconds (934.77 seconds total)