Starting phenix.real_space_refine
on Wed Jun  4 20:52:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j8b_61226/06_2025/9j8b_61226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j8b_61226/06_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_61226/06_2025/9j8b_61226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j8b_61226/06_2025/9j8b_61226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j8b_61226/06_2025/9j8b_61226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j8b_61226/06_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-5710/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: 3.20, per 1000 atoms: 0.77
  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: 1.05
  Conformation dependent library (CDL) restraints added in 466.5 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: 0.48
  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: 1.04

  Time building geometry restraints manager: 1.24 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:             0.980
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.480
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.590
-------------------------------------------------------------------------------
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  : 0.420 
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: 0.1473
  time to fit residues: 24.4274
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  : 0.465 
-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.142583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.117345 restraints weight = 6752.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120397 restraints weight = 4011.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.122696 restraints weight = 2906.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
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       4.36021 (  609)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       1.50130 (    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  : 0.477 
Fit side-chains
REVERT: A  424 GLU cc_start: 0.8594 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: A  428 THR cc_start: 0.8817 (m) cc_final: 0.8390 (m)
REVERT: A  430 ILE cc_start: 0.8145 (tt) cc_final: 0.7856 (tp)
  outliers start: 11
  outliers final: 5
  residues processed: 125
  average time/residue: 0.1313
  time to fit residues: 21.9370
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  : 0.542 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.7742

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.139544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.113824 restraints weight = 6658.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.117043 restraints weight = 3953.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.119293 restraints weight = 2831.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2277

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= 0.130
  Angle     :  0.584   7.420   5855  Z= 0.295
  Chirality :  0.039   0.133    647
  Planarity :  0.004   0.038    719
  Dihedral  :  3.831  19.829    572
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.08 %
    Favored  : 79.95 %
  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:  1.01 (0.30), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.24 (0.50), 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 173 
 PHE   0.015   0.001   PHE A 531 
 TYR   0.021   0.001   TYR A 549 
 ARG   0.006   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04070 (  213)
  hydrogen bonds       : angle       4.13765 (  609)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       1.05256 (    2)
  covalent geometry    : bond        0.00301 ( 4291)
  covalent geometry    : angle       0.58425 ( 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
  123 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.613 
Fit side-chains
REVERT: A  402 LEU cc_start: 0.7935 (tp) cc_final: 0.7571 (tp)
REVERT: A  419 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8206 (mt0)
REVERT: A  424 GLU cc_start: 0.8593 (tm-30) cc_final: 0.7955 (tm-30)
REVERT: A  428 THR cc_start: 0.8749 (m) cc_final: 0.8301 (m)
REVERT: A  430 ILE cc_start: 0.8154 (tt) cc_final: 0.7851 (tp)
  outliers start: 13
  outliers final: 5
  residues processed: 116
  average time/residue: 0.1492
  time to fit residues: 23.1593
Evaluate side-chains
  113 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0980
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.5782

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.140050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.114364 restraints weight = 6627.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.117759 restraints weight = 3867.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.120093 restraints weight = 2748.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2529

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= 0.120
  Angle     :  0.594   8.607   5855  Z= 0.292
  Chirality :  0.040   0.286    647
  Planarity :  0.004   0.036    719
  Dihedral  :  3.741  20.109    572
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 20.27 %
    Favored  : 78.13 %
  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:  0.53 (0.40), residues: 518
  helix:  1.12 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.15 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 170 
 HIS   0.001   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        0.03716 (  213)
  hydrogen bonds       : angle       4.03715 (  609)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.98379 (    2)
  covalent geometry    : bond        0.00274 ( 4291)
  covalent geometry    : angle       0.59371 ( 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
  114 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A  424 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7981 (tm-30)
REVERT: A  428 THR cc_start: 0.8778 (m) cc_final: 0.8330 (m)
REVERT: A  430 ILE cc_start: 0.8104 (tt) cc_final: 0.7801 (tp)
REVERT: A  598 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7809 (mmm-85)
  outliers start: 7
  outliers final: 3
  residues processed: 110
  average time/residue: 0.1395
  time to fit residues: 19.7353
Evaluate side-chains
  106 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   chunk 4 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 51 optimal weight:    0.2980
   chunk 37 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 143 ASN
A 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.146953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.121709 restraints weight = 6918.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.125165 restraints weight = 3969.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.127371 restraints weight = 2776.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2717

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= 0.118
  Angle     :  0.589   8.845   5855  Z= 0.290
  Chirality :  0.038   0.126    647
  Planarity :  0.004   0.035    719
  Dihedral  :  3.730  19.817    572
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.27 %
    Favored  : 77.45 %
  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:  0.62 (0.40), residues: 518
  helix:  1.16 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.04 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 607 
 PHE   0.013   0.001   PHE A 531 
 TYR   0.019   0.001   TYR A 549 
 ARG   0.010   0.001   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  213)
  hydrogen bonds       : angle       3.88038 (  609)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       0.94734 (    2)
  covalent geometry    : bond        0.00274 ( 4291)
  covalent geometry    : angle       0.58878 ( 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
  116 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A  143 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8214 (m-40)
REVERT: A  424 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8033 (tm-30)
REVERT: A  428 THR cc_start: 0.8820 (m) cc_final: 0.8352 (m)
REVERT: A  430 ILE cc_start: 0.8081 (tt) cc_final: 0.7765 (tp)
REVERT: A  598 ARG cc_start: 0.8154 (mmt180) cc_final: 0.7832 (mmm-85)
  outliers start: 10
  outliers final: 6
  residues processed: 113
  average time/residue: 0.1239
  time to fit residues: 18.7352
Evaluate side-chains
  109 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
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  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:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0980
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.139677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.113552 restraints weight = 6620.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.116861 restraints weight = 3995.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.119010 restraints weight = 2869.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2827

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= 0.120
  Angle     :  0.591   8.480   5855  Z= 0.291
  Chirality :  0.040   0.269    647
  Planarity :  0.004   0.034    719
  Dihedral  :  3.674  19.812    572
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  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: 342
  sheet:  None (None), residues: 0
  loop : -1.12 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 370 
 PHE   0.012   0.001   PHE A 109 
 TYR   0.019   0.001   TYR A 316 
 ARG   0.007   0.001   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03480 (  213)
  hydrogen bonds       : angle       3.83777 (  609)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.83778 (    2)
  covalent geometry    : bond        0.00275 ( 4291)
  covalent geometry    : angle       0.59099 ( 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
  119 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  424 GLU cc_start: 0.8576 (tm-30) cc_final: 0.7983 (tm-30)
REVERT: A  428 THR cc_start: 0.8822 (m) cc_final: 0.8373 (m)
REVERT: A  430 ILE cc_start: 0.8075 (tt) cc_final: 0.7765 (tp)
REVERT: A  598 ARG cc_start: 0.8199 (mmt180) cc_final: 0.7880 (mmm-85)
  outliers start: 12
  outliers final: 7
  residues processed: 113
  average time/residue: 0.2130
  time to fit residues: 32.4036
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  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  493 ILE
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:    0.5980
   chunk 42 optimal weight:    0.0670
   chunk 19 optimal weight:    4.9990
   chunk 50 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6320

-------------------------------------------------------------------------------
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 419 GLN
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.145856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.121147 restraints weight = 6825.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.124441 restraints weight = 4044.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.126772 restraints weight = 2875.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3004

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= 0.118
  Angle     :  0.587   8.318   5855  Z= 0.289
  Chirality :  0.039   0.141    647
  Planarity :  0.004   0.035    719
  Dihedral  :  3.699  19.363    572
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.32 %
    Favored  : 75.17 %
  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:  0.77 (0.40), residues: 518
  helix:  1.32 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.11 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 370 
 PHE   0.016   0.001   PHE A 408 
 TYR   0.016   0.001   TYR A 549 
 ARG   0.008   0.001   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03360 (  213)
  hydrogen bonds       : angle       3.79283 (  609)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.81574 (    2)
  covalent geometry    : bond        0.00276 ( 4291)
  covalent geometry    : angle       0.58676 ( 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
  118 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A  212 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7201 (mp0)
REVERT: A  366 PHE cc_start: 0.8437 (t80) cc_final: 0.8051 (t80)
REVERT: A  424 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8019 (tm-30)
REVERT: A  428 THR cc_start: 0.8824 (m) cc_final: 0.8332 (m)
REVERT: A  430 ILE cc_start: 0.8103 (tt) cc_final: 0.7792 (tp)
REVERT: A  588 GLN cc_start: 0.8122 (tp40) cc_final: 0.7361 (tp-100)
REVERT: A  598 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7865 (mmm-85)
  outliers start: 11
  outliers final: 8
  residues processed: 113
  average time/residue: 0.1472
  time to fit residues: 22.1468
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  : 0.466 
-------------------------------------------------------------------------------
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  131 MET
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  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:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0870
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 370 HIS
A 419 GLN
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.146286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.121358 restraints weight = 6624.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.124621 restraints weight = 4021.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.126909 restraints weight = 2891.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.3110

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= 0.119
  Angle     :  0.593   7.716   5855  Z= 0.292
  Chirality :  0.040   0.275    647
  Planarity :  0.004   0.033    719
  Dihedral  :  3.645  19.454    572
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  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:  0.78 (0.40), residues: 518
  helix:  1.33 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.10 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 170 
 HIS   0.003   0.001   HIS A 370 
 PHE   0.015   0.001   PHE A 109 
 TYR   0.026   0.001   TYR A 549 
 ARG   0.005   0.000   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03292 (  213)
  hydrogen bonds       : angle       3.78848 (  609)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.86447 (    2)
  covalent geometry    : bond        0.00279 ( 4291)
  covalent geometry    : angle       0.59289 ( 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
  117 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  366 PHE cc_start: 0.8474 (t80) cc_final: 0.8068 (t80)
REVERT: A  424 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: A  430 ILE cc_start: 0.8099 (tt) cc_final: 0.7817 (tp)
REVERT: A  588 GLN cc_start: 0.8174 (tp40) cc_final: 0.7408 (tp-100)
REVERT: A  598 ARG cc_start: 0.8174 (mmt180) cc_final: 0.7813 (mmm-85)
  outliers start: 11
  outliers final: 7
  residues processed: 112
  average time/residue: 0.1754
  time to fit residues: 26.9510
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  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  131 MET
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  526 SER
Chi-restraints excluded: chain A residue  537 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 369 ASN
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 = 0.3600 r_free = 0.3600 target = 0.143807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.118578 restraints weight = 6755.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.121869 restraints weight = 4098.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.124143 restraints weight = 2942.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3166

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= 0.127
  Angle     :  0.598   8.370   5855  Z= 0.293
  Chirality :  0.039   0.136    647
  Planarity :  0.004   0.033    719
  Dihedral  :  3.639  19.515    572
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.46 %
    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 (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:  0.77 (0.40), residues: 518
  helix:  1.33 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.11 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 548 
 PHE   0.015   0.001   PHE A 109 
 TYR   0.026   0.001   TYR A 549 
 ARG   0.005   0.000   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03393 (  213)
  hydrogen bonds       : angle       3.82211 (  609)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.88727 (    2)
  covalent geometry    : bond        0.00299 ( 4291)
  covalent geometry    : angle       0.59782 ( 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
  118 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  424 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8161 (tm-30)
REVERT: A  430 ILE cc_start: 0.8117 (tt) cc_final: 0.7857 (tp)
REVERT: A  588 GLN cc_start: 0.8177 (tp40) cc_final: 0.7474 (tp-100)
REVERT: A  598 ARG cc_start: 0.8169 (mmt180) cc_final: 0.7809 (mmm-85)
  outliers start: 12
  outliers final: 7
  residues processed: 113
  average time/residue: 0.1576
  time to fit residues: 24.0352
Evaluate side-chains
  112 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  495 TYR
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  537 THR
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:    0.9980
   chunk 42 optimal weight:    0.0970
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:   10.0000
   chunk 6 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0060
   overall best weight:    0.4194

-------------------------------------------------------------------------------
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 369 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 = 0.3621 r_free = 0.3621 target = 0.145428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120244 restraints weight = 6744.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.123457 restraints weight = 4034.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.125903 restraints weight = 2896.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.3214

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= 0.117
  Angle     :  0.615   8.856   5855  Z= 0.298
  Chirality :  0.040   0.163    647
  Planarity :  0.004   0.033    719
  Dihedral  :  3.630  19.260    572
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 24.37 %
    Favored  : 74.49 %
  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:  1.34 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.11 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 548 
 PHE   0.013   0.001   PHE A 408 
 TYR   0.025   0.001   TYR A 549 
 ARG   0.006   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03232 (  213)
  hydrogen bonds       : angle       3.79412 (  609)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.83536 (    2)
  covalent geometry    : bond        0.00266 ( 4291)
  covalent geometry    : angle       0.61519 ( 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
  110 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  212 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7151 (mp0)
REVERT: A  424 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: A  430 ILE cc_start: 0.8121 (tt) cc_final: 0.7818 (tp)
REVERT: A  588 GLN cc_start: 0.8194 (tp40) cc_final: 0.7515 (tp-100)
REVERT: A  598 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7827 (mmm-85)
  outliers start: 5
  outliers final: 4
  residues processed: 107
  average time/residue: 0.1975
  time to fit residues: 28.4879
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  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0770
   chunk 41 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 369 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 = 0.3555 r_free = 0.3555 target = 0.141213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.114363 restraints weight = 6689.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.117584 restraints weight = 4136.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.119920 restraints weight = 3029.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3243

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= 0.116
  Angle     :  0.607   8.995   5855  Z= 0.294
  Chirality :  0.040   0.237    647
  Planarity :  0.004   0.033    719
  Dihedral  :  3.593  19.296    572
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 24.37 %
    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:  0.80 (0.40), residues: 518
  helix:  1.36 (0.30), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.14 (0.50), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 548 
 PHE   0.013   0.001   PHE A 408 
 TYR   0.013   0.001   TYR A 549 
 ARG   0.006   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03239 (  213)
  hydrogen bonds       : angle       3.78057 (  609)
  SS BOND              : bond        0.00044 (    1)
  SS BOND              : angle       0.85085 (    2)
  covalent geometry    : bond        0.00268 ( 4291)
  covalent geometry    : angle       0.60666 ( 5853)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2173.51 seconds
wall clock time: 40 minutes 25.48 seconds (2425.48 seconds total)