Starting phenix.real_space_refine
on Sat May 10 11:17:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smp_40598/05_2025/8smp_40598.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smp_40598/05_2025/8smp_40598.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smp_40598/05_2025/8smp_40598.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smp_40598/05_2025/8smp_40598.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smp_40598/05_2025/8smp_40598.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smp_40598/05_2025/8smp_40598.cif"
  }
  resolution = 3.4
  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=  -0.000 sd=   0.040
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      48      5.16       5
     C    3949      2.51       5
     N     989      2.21       5
     O    1108      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6097
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4339
          Classifications: {'peptide': 527}
          Link IDs: {'PTRANS': 14, 'TRANS': 512}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 937
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 795
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.05, per 1000 atoms: 0.66
  Number of scatterers: 6097
  At special positions: 0
  Unit cell: (68.04, 78.84, 138.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P       2     15.00
     Mg      1     11.99
     O    1108      8.00
     N     989      7.00
     C    3949      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " 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: 1.44
  Conformation dependent library (CDL) restraints added in 795.9 milliseconds
  

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 6 sheets defined
      46.2% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 52
    Processing helix  chain 'A' and resid 59 through 90
    Processing helix  chain 'A' and resid 110 through 123
    Processing helix  chain 'A' and resid 127 through 129
      No H-bonds generated for 'chain 'A' and resid 127 through 129'
    Processing helix  chain 'A' and resid 144 through 155
      removed outlier: 4.027A  pdb=" N   MET A 148 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 206
    Processing helix  chain 'A' and resid 216 through 230
      removed outlier: 3.980A  pdb=" N   GLU A 220 " --> pdb=" O   GLY A 216 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A 221 " --> pdb=" O   GLY A 217 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 259
    Processing helix  chain 'A' and resid 278 through 294
      removed outlier: 3.632A  pdb=" N   PHE A 282 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 302
      removed outlier: 3.509A  pdb=" N   PHE A 302 " --> pdb=" O   CYS A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 329
      removed outlier: 4.917A  pdb=" N   GLU A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   ALA A 326 " --> pdb=" O   VAL A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 352
    Processing helix  chain 'A' and resid 371 through 394
      removed outlier: 3.883A  pdb=" N   LEU A 391 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR A 392 " --> pdb=" O   ARG A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 428
      Proline residue:  A 415  - end of helix
    Processing helix  chain 'A' and resid 430 through 457
    Processing helix  chain 'A' and resid 459 through 465
      removed outlier: 3.755A  pdb=" N   LEU A 462 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER A 465 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 472
      removed outlier: 3.981A  pdb=" N   LEU A 470 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 485
    Processing helix  chain 'A' and resid 505 through 529
    Processing helix  chain 'A' and resid 534 through 568
    Processing helix  chain 'H' and resid 31 through 34
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.723A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164
      removed outlier: 6.416A  pdb=" N   GLY A 161 " --> pdb=" O   CYS A 210 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   MET A 212 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   TYR A 163 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL A 100 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ILE A 134 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   LEU A 102 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   VAL A 136 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   ILE A 104 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   ASP A 138 " --> pdb=" O   ILE A 104 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   GLY A 106 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA A 105 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY A 313 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   GLY A 264 " --> pdb=" O   ARG A 316 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   TYR A 263 " --> pdb=" O   THR A 356 " (cutoff:3.500A)
      removed outlier: 10.447A  pdb=" N   TYR A 358 " --> pdb=" O   TYR A 263 " (cutoff:3.500A)
      removed outlier: 10.868A  pdb=" N   ALA A 265 " --> pdb=" O   TYR A 358 " (cutoff:3.500A)
      removed outlier: 11.457A  pdb=" N   HIS A 360 " --> pdb=" O   ALA A 265 " (cutoff:3.500A)
      removed outlier: 10.434A  pdb=" N   GLY A 267 " --> pdb=" O   HIS A 360 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   SER A 362 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA3, first strand: chain 'H' and resid 13 through 15
      removed outlier: 3.586A  pdb=" N   ALA H  95 " --> pdb=" O   VAL H 122 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 13
      removed outlier: 6.561A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.575A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    966 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: 1.91

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1720
        1.34 -     1.45: 1185
        1.45 -     1.57: 3276
        1.57 -     1.69: 3
        1.69 -     1.81: 77
  Bond restraints: 6261
  Sorted by residual:
  bond pdb=" N   THR A  25 "
       pdb=" CA  THR A  25 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.29e-02 6.01e+03 5.63e+00
  bond pdb=" N   HIS A  23 "
       pdb=" CA  HIS A  23 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.41e-02 5.03e+03 4.00e+00
  bond pdb=" C   HIS A  23 "
       pdb=" N   PRO A  24 "
    ideal  model  delta    sigma   weight residual
    1.326  1.351 -0.025 1.44e-02 4.82e+03 3.03e+00
  bond pdb=" CG  HIS A  23 "
       pdb=" CD2 HIS A  23 "
    ideal  model  delta    sigma   weight residual
    1.354  1.338  0.016 1.10e-02 8.26e+03 2.08e+00
  bond pdb=" N   THR A 335 "
       pdb=" CA  THR A 335 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.013 1.29e-02 6.01e+03 1.07e+00
  ... (remaining 6256 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 8384
        1.89 -     3.79: 90
        3.79 -     5.68: 17
        5.68 -     7.58: 1
        7.58 -     9.47: 3
  Bond angle restraints: 8495
  Sorted by residual:
  angle pdb=" C   GLY A 334 "
        pdb=" N   THR A 335 "
        pdb=" CA  THR A 335 "
      ideal   model   delta    sigma   weight residual
     121.54  131.01   -9.47 1.91e+00 2.74e-01 2.46e+01
  angle pdb=" N   ILE A 460 "
        pdb=" CA  ILE A 460 "
        pdb=" C   ILE A 460 "
      ideal   model   delta    sigma   weight residual
     113.07  106.49    6.58 1.36e+00 5.41e-01 2.34e+01
  angle pdb=" N   VAL H  67 "
        pdb=" CA  VAL H  67 "
        pdb=" C   VAL H  67 "
      ideal   model   delta    sigma   weight residual
     112.96  109.89    3.07 1.00e+00 1.00e+00 9.42e+00
  angle pdb=" N   THR A 335 "
        pdb=" CA  THR A 335 "
        pdb=" CB  THR A 335 "
      ideal   model   delta    sigma   weight residual
     110.49  115.34   -4.85 1.69e+00 3.50e-01 8.23e+00
  angle pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
        pdb=" CA  ALA L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  126.93   -5.39 1.91e+00 2.74e-01 7.96e+00
  ... (remaining 8490 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3141
       17.79 -    35.58: 379
       35.58 -    53.37: 115
       53.37 -    71.16: 13
       71.16 -    88.95: 3
  Dihedral angle restraints: 3651
    sinusoidal: 1441
      harmonic: 2210
  Sorted by residual:
  dihedral pdb=" CA  ASN A 458 "
           pdb=" C   ASN A 458 "
           pdb=" N   PHE A 459 "
           pdb=" CA  PHE A 459 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.33   17.67     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" N   ASN H  80 "
           pdb=" CA  ASN H  80 "
           pdb=" CB  ASN H  80 "
           pdb=" CG  ASN H  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.96   59.96     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   LYS A 537 "
           pdb=" CA  LYS A 537 "
           pdb=" CB  LYS A 537 "
           pdb=" CG  LYS A 537 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.60  -59.40     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3648 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 642
       0.035 -    0.069: 194
       0.069 -    0.104: 61
       0.104 -    0.139: 21
       0.139 -    0.173: 3
  Chirality restraints: 921
  Sorted by residual:
  chirality pdb=" CA  HIS A  23 "
            pdb=" N   HIS A  23 "
            pdb=" C   HIS A  23 "
            pdb=" CB  HIS A  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.51e-01
  chirality pdb=" CA  TRP A 436 "
            pdb=" N   TRP A 436 "
            pdb=" C   TRP A 436 "
            pdb=" CB  TRP A 436 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.60e-01
  chirality pdb=" CA  ILE A 460 "
            pdb=" N   ILE A 460 "
            pdb=" C   ILE A 460 "
            pdb=" CB  ILE A 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 918 not shown)

  Planarity restraints: 1036
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  59 "   -0.044 5.00e-02 4.00e+02   6.59e-02 6.94e+00
        pdb=" N   PRO L  60 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO L  60 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO L  60 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 534 "   -0.030 5.00e-02 4.00e+02   4.63e-02 3.42e+00
        pdb=" N   PRO A 535 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 535 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 535 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 310 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.19e+00
        pdb=" N   PRO A 311 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 311 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 311 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1033 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 291
        2.73 -     3.27: 5741
        3.27 -     3.81: 10224
        3.81 -     4.36: 11622
        4.36 -     4.90: 21170
  Nonbonded interactions: 49048
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 334 "
            pdb=" OG1 THR A 335 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O   LYS A  17 "
            pdb=" OH  TYR A 354 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O2B UDP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.263 2.170
  nonbonded pdb=" O   MET A 469 "
            pdb=" OG1 THR A 473 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OE2 GLU A 109 "
            pdb=" NH1 ARG A 496 "
     model   vdw
     2.286 3.120
  ... (remaining 49043 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.730
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     17.100
  Find NCS groups from input model:        0.080
  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:2.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
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      :  0.002   0.038   6263  Z= 0.117
  Angle     :  0.526   9.475   8499  Z= 0.285
  Chirality :  0.040   0.173    921
  Planarity :  0.004   0.066   1036
  Dihedral  : 16.401  88.946   2241
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.15 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 22.42 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.32), residues: 747
  helix:  2.34 (0.29), residues: 338
  sheet:  0.32 (0.41), residues: 168
  loop : -1.27 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 432 
 HIS   0.002   0.000   HIS A  72 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.011   0.001   TYR A 451 
 ARG   0.002   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12115 (  338)
  hydrogen bonds       : angle       4.85189 (  966)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       0.71426 (    4)
  covalent geometry    : bond        0.00226 ( 6261)
  covalent geometry    : angle       0.52594 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  436 TRP cc_start: 0.8110 (m100) cc_final: 0.7854 (m100)
REVERT: H   93 ASP cc_start: 0.8716 (m-30) cc_final: 0.8337 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 123
  average time/residue: 0.1846
  time to fit residues: 29.6754
Evaluate side-chains
  120 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   92 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0370
   chunk 35 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
L  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.136300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.116339 restraints weight = 7801.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.57
r_work: 0.3080 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6263  Z= 0.145
  Angle     :  0.528  11.497   8499  Z= 0.281
  Chirality :  0.041   0.141    921
  Planarity :  0.005   0.049   1036
  Dihedral  :  4.527  41.309    872
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.95 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 21.21 %
    Favored  : 76.52 %
  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:  1.14 (0.32), residues: 747
  helix:  2.31 (0.28), residues: 338
  sheet:  0.39 (0.40), residues: 169
  loop : -1.28 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 432 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.016   0.001   TYR H  83 
 ARG   0.006   0.000   ARG A 496 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04084 (  338)
  hydrogen bonds       : angle       3.95060 (  966)
  SS BOND              : bond        0.00222 (    2)
  SS BOND              : angle       0.54607 (    4)
  covalent geometry    : bond        0.00337 ( 6261)
  covalent geometry    : angle       0.52798 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  284 SER cc_start: 0.9003 (m) cc_final: 0.8755 (m)
REVERT: A  436 TRP cc_start: 0.8448 (m100) cc_final: 0.8202 (m100)
REVERT: L   93 SER cc_start: 0.8224 (t) cc_final: 0.7939 (p)
  outliers start: 15
  outliers final: 7
  residues processed: 126
  average time/residue: 0.2410
  time to fit residues: 39.8810
Evaluate side-chains
  123 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   chunk 73 optimal weight:    0.0570
   chunk 42 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.0504

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 260 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.131539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.112108 restraints weight = 7879.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.47
r_work: 0.3023 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6263  Z= 0.182
  Angle     :  0.567  11.295   8499  Z= 0.301
  Chirality :  0.042   0.148    921
  Planarity :  0.004   0.052   1036
  Dihedral  :  4.646  36.355    869
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.69 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.97 %
    Favored  : 74.70 %
  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 (0.31), residues: 747
  helix:  2.08 (0.28), residues: 334
  sheet:  0.17 (0.40), residues: 172
  loop : -1.45 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 432 
 HIS   0.004   0.001   HIS A 398 
 PHE   0.023   0.002   PHE A 323 
 TYR   0.022   0.001   TYR H  83 
 ARG   0.002   0.000   ARG A 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04669 (  338)
  hydrogen bonds       : angle       4.06076 (  966)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       0.67023 (    4)
  covalent geometry    : bond        0.00431 ( 6261)
  covalent geometry    : angle       0.56673 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A   60 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.4950 (m-10)
  outliers start: 22
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1849
  time to fit residues: 30.9127
Evaluate side-chains
  120 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  125 SER
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    0.0970
   chunk 53 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 58 optimal weight:    0.4980
   chunk 51 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0040
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.3790

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

Flipped N/Q/H residues before XYZ refinement:
L  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.135666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.115396 restraints weight = 7857.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.42
r_work: 0.3079 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6263  Z= 0.106
  Angle     :  0.501  11.355   8499  Z= 0.262
  Chirality :  0.040   0.135    921
  Planarity :  0.004   0.048   1036
  Dihedral  :  4.343  33.420    869
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.79 %
    Favored  : 73.48 %
  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:  1.08 (0.32), residues: 747
  helix:  2.30 (0.28), residues: 337
  sheet:  0.30 (0.40), residues: 171
  loop : -1.32 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 432 
 HIS   0.002   0.001   HIS A  72 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.013   0.001   TYR H  83 
 ARG   0.002   0.000   ARG A 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (  338)
  hydrogen bonds       : angle       3.74924 (  966)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       0.61731 (    4)
  covalent geometry    : bond        0.00231 ( 6261)
  covalent geometry    : angle       0.50108 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  194 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7424 (pt0)
REVERT: A  436 TRP cc_start: 0.8422 (m100) cc_final: 0.7989 (m100)
REVERT: A  461 MET cc_start: 0.8067 (mmp) cc_final: 0.7716 (mmp)
REVERT: L   80 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8212 (mm-40)
  outliers start: 18
  outliers final: 11
  residues processed: 125
  average time/residue: 0.1950
  time to fit residues: 31.9614
Evaluate side-chains
  121 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  125 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.133583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.114449 restraints weight = 7813.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.37
r_work: 0.3072 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6263  Z= 0.131
  Angle     :  0.524  11.266   8499  Z= 0.274
  Chirality :  0.040   0.138    921
  Planarity :  0.004   0.049   1036
  Dihedral  :  4.377  34.827    869
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.69 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.09 %
    Favored  : 72.12 %
  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:  1.04 (0.31), residues: 747
  helix:  2.26 (0.28), residues: 336
  sheet:  0.30 (0.40), residues: 171
  loop : -1.33 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 432 
 HIS   0.002   0.001   HIS A 398 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.016   0.001   TYR H  83 
 ARG   0.002   0.000   ARG A 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03975 (  338)
  hydrogen bonds       : angle       3.78916 (  966)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       0.61525 (    4)
  covalent geometry    : bond        0.00300 ( 6261)
  covalent geometry    : angle       0.52397 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A   60 PHE cc_start: 0.5377 (OUTLIER) cc_final: 0.4746 (m-10)
REVERT: A  194 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7499 (pt0)
REVERT: A  436 TRP cc_start: 0.8476 (m100) cc_final: 0.8041 (m100)
  outliers start: 25
  outliers final: 15
  residues processed: 125
  average time/residue: 0.1875
  time to fit residues: 31.0598
Evaluate side-chains
  125 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  125 SER
Chi-restraints excluded: chain L residue    5 MET
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 49 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 39 optimal weight:    0.7980
   chunk 67 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:
L  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.133877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.113883 restraints weight = 7702.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 1.39
r_work: 0.3056 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6263  Z= 0.125
  Angle     :  0.520  11.145   8499  Z= 0.270
  Chirality :  0.040   0.139    921
  Planarity :  0.004   0.049   1036
  Dihedral  :  4.392  33.920    869
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.15 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 25.00 %
    Favored  : 71.52 %
  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:  1.10 (0.31), residues: 747
  helix:  2.30 (0.28), residues: 336
  sheet:  0.36 (0.40), residues: 171
  loop : -1.32 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 432 
 HIS   0.002   0.001   HIS A 398 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.016   0.001   TYR H  83 
 ARG   0.002   0.000   ARG A 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03886 (  338)
  hydrogen bonds       : angle       3.75559 (  966)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       0.60830 (    4)
  covalent geometry    : bond        0.00286 ( 6261)
  covalent geometry    : angle       0.52023 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A   60 PHE cc_start: 0.5404 (OUTLIER) cc_final: 0.4742 (m-10)
REVERT: A  194 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7580 (pt0)
REVERT: A  436 TRP cc_start: 0.8482 (m100) cc_final: 0.8132 (m100)
REVERT: L   80 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8246 (mm-40)
  outliers start: 23
  outliers final: 18
  residues processed: 122
  average time/residue: 0.1970
  time to fit residues: 31.4258
Evaluate side-chains
  125 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue    5 MET
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 73 optimal weight:    0.0170
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 68 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.6220

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.133657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.114160 restraints weight = 7828.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.35
r_work: 0.3069 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6263  Z= 0.128
  Angle     :  0.527  11.129   8499  Z= 0.272
  Chirality :  0.040   0.137    921
  Planarity :  0.004   0.049   1036
  Dihedral  :  4.405  33.989    869
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.42 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 24.85 %
    Favored  : 71.52 %
  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:  1.09 (0.31), residues: 747
  helix:  2.33 (0.28), residues: 334
  sheet:  0.40 (0.39), residues: 171
  loop : -1.39 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 432 
 HIS   0.002   0.001   HIS A 398 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.002   0.000   ARG A 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  338)
  hydrogen bonds       : angle       3.76770 (  966)
  SS BOND              : bond        0.00162 (    2)
  SS BOND              : angle       0.61191 (    4)
  covalent geometry    : bond        0.00293 ( 6261)
  covalent geometry    : angle       0.52660 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.649 
Fit side-chains
REVERT: A   60 PHE cc_start: 0.5267 (OUTLIER) cc_final: 0.4694 (m-10)
REVERT: A  194 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7512 (pt0)
REVERT: A  436 TRP cc_start: 0.8442 (m100) cc_final: 0.8026 (m100)
  outliers start: 24
  outliers final: 19
  residues processed: 126
  average time/residue: 0.1824
  time to fit residues: 30.0953
Evaluate side-chains
  126 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue    5 MET
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 65 optimal weight:    0.4980
   chunk 70 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 25 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:
L  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.132853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.113342 restraints weight = 7773.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.34
r_work: 0.3059 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6263  Z= 0.141
  Angle     :  0.540  11.111   8499  Z= 0.280
  Chirality :  0.041   0.139    921
  Planarity :  0.004   0.049   1036
  Dihedral  :  4.466  34.232    869
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 24.70 %
    Favored  : 71.06 %
  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:  1.04 (0.31), residues: 747
  helix:  2.27 (0.28), residues: 334
  sheet:  0.40 (0.39), residues: 171
  loop : -1.42 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 432 
 HIS   0.003   0.001   HIS A 398 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.016   0.001   TYR H  83 
 ARG   0.001   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04067 (  338)
  hydrogen bonds       : angle       3.81475 (  966)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       0.63597 (    4)
  covalent geometry    : bond        0.00328 ( 6261)
  covalent geometry    : angle       0.53965 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A   60 PHE cc_start: 0.5307 (OUTLIER) cc_final: 0.4630 (m-10)
REVERT: A  194 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7544 (pt0)
REVERT: A  436 TRP cc_start: 0.8442 (m100) cc_final: 0.8054 (m100)
  outliers start: 28
  outliers final: 21
  residues processed: 127
  average time/residue: 0.1804
  time to fit residues: 30.2943
Evaluate side-chains
  128 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  125 SER
Chi-restraints excluded: chain L residue    5 MET
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0870
   overall best weight:    0.7358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.133002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.112627 restraints weight = 7793.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.44
r_work: 0.3043 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6263  Z= 0.141
  Angle     :  0.545  11.060   8499  Z= 0.282
  Chirality :  0.041   0.138    921
  Planarity :  0.004   0.049   1036
  Dihedral  :  4.487  33.969    869
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 24.55 %
    Favored  : 71.36 %
  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:  1.03 (0.31), residues: 747
  helix:  2.25 (0.28), residues: 334
  sheet:  0.44 (0.40), residues: 171
  loop : -1.45 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 432 
 HIS   0.003   0.001   HIS A 398 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.016   0.001   TYR H  83 
 ARG   0.001   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04098 (  338)
  hydrogen bonds       : angle       3.83252 (  966)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       0.64296 (    4)
  covalent geometry    : bond        0.00328 ( 6261)
  covalent geometry    : angle       0.54468 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A   60 PHE cc_start: 0.5321 (OUTLIER) cc_final: 0.4600 (m-10)
REVERT: A  194 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7556 (pt0)
REVERT: A  436 TRP cc_start: 0.8480 (m100) cc_final: 0.8115 (m100)
  outliers start: 27
  outliers final: 19
  residues processed: 122
  average time/residue: 0.1796
  time to fit residues: 28.9487
Evaluate side-chains
  126 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  125 SER
Chi-restraints excluded: chain L residue    5 MET
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0770
   chunk 59 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0370
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
L  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.133611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.113993 restraints weight = 7824.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.35
r_work: 0.3067 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6263  Z= 0.127
  Angle     :  0.539  11.034   8499  Z= 0.278
  Chirality :  0.040   0.135    921
  Planarity :  0.004   0.049   1036
  Dihedral  :  4.433  33.364    869
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.15 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.15 %
    Favored  : 71.21 %
  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:  1.09 (0.31), residues: 747
  helix:  2.30 (0.28), residues: 334
  sheet:  0.48 (0.40), residues: 171
  loop : -1.42 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 432 
 HIS   0.002   0.001   HIS A 398 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.002   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  338)
  hydrogen bonds       : angle       3.79069 (  966)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       0.63269 (    4)
  covalent geometry    : bond        0.00290 ( 6261)
  covalent geometry    : angle       0.53932 ( 8495)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.645 
Fit side-chains
REVERT: A   60 PHE cc_start: 0.5260 (OUTLIER) cc_final: 0.4604 (m-10)
REVERT: A  194 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7500 (pt0)
REVERT: A  436 TRP cc_start: 0.8449 (m100) cc_final: 0.8092 (m100)
  outliers start: 24
  outliers final: 21
  residues processed: 121
  average time/residue: 0.1774
  time to fit residues: 28.4755
Evaluate side-chains
  129 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  125 SER
Chi-restraints excluded: chain L residue    5 MET
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.132544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.112779 restraints weight = 7980.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.37
r_work: 0.3048 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6263  Z= 0.145
  Angle     :  0.559  10.987   8499  Z= 0.288
  Chirality :  0.041   0.140    921
  Planarity :  0.004   0.050   1036
  Dihedral  :  4.517  34.128    869
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.95 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 25.30 %
    Favored  : 71.21 %
  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:  0.99 (0.31), residues: 747
  helix:  2.22 (0.28), residues: 334
  sheet:  0.45 (0.40), residues: 171
  loop : -1.48 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 432 
 HIS   0.003   0.001   HIS A 398 
 PHE   0.022   0.001   PHE A 323 
 TYR   0.016   0.001   TYR H  83 
 ARG   0.002   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  338)
  hydrogen bonds       : angle       3.84741 (  966)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       0.62465 (    4)
  covalent geometry    : bond        0.00337 ( 6261)
  covalent geometry    : angle       0.55911 ( 8495)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3272.13 seconds
wall clock time: 57 minutes 29.47 seconds (3449.47 seconds total)