Starting phenix.real_space_refine
on Sun Apr 27 16:41:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gz2_51720/04_2025/9gz2_51720.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gz2_51720/04_2025/9gz2_51720.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gz2_51720/04_2025/9gz2_51720.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gz2_51720/04_2025/9gz2_51720.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gz2_51720/04_2025/9gz2_51720.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gz2_51720/04_2025/9gz2_51720.cif"
  }
  resolution = 2.9
  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=  -0.000 sd=   0.080
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       3      5.49       5
     Mg      1      5.21       5
     S      32      5.16       5
     C    3956      2.51       5
     N    1054      2.21       5
     O    1154      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6200
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 764, 6147
          Classifications: {'peptide': 764}
          Link IDs: {'PTRANS': 29, 'TRANS': 734}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 53
          Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'XB2': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 4.90, per 1000 atoms: 0.79
  Number of scatterers: 6200
  At special positions: 0
  Unit cell: (69.87, 92.886, 124.122, 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      32     16.00
     P       3     15.00
     Mg      1     11.99
     O    1154      8.00
     N    1054      7.00
     C    3956      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.66
  Conformation dependent library (CDL) restraints added in 879.5 milliseconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1434

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 7 sheets defined
      55.0% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
      removed outlier: 3.510A  pdb=" N   MET A   6 " --> pdb=" O   ASP A   3 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A   7 " --> pdb=" O   SER A   4 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ALA A  11 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      Proline residue:  A  14  - end of helix
    Processing helix  chain 'A' and resid 19 through 27
      removed outlier: 3.678A  pdb=" N   GLU A  25 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 89 through 93
    Processing helix  chain 'A' and resid 97 through 110
    Processing helix  chain 'A' and resid 135 through 143
    Processing helix  chain 'A' and resid 153 through 169
    Processing helix  chain 'A' and resid 183 through 202
    Processing helix  chain 'A' and resid 215 through 231
      removed outlier: 3.503A  pdb=" N   ILE A 221 " --> pdb=" O   GLU A 217 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ASN A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      Proline residue:  A 225  - end of helix
      removed outlier: 4.000A  pdb=" N   PHE A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 274
    Processing helix  chain 'A' and resid 283 through 292
      removed outlier: 4.199A  pdb=" N   TYR A 287 " --> pdb=" O   TYR A 283 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 290 " --> pdb=" O   PHE A 286 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASN A 292 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 301
    Processing helix  chain 'A' and resid 306 through 309
      removed outlier: 3.854A  pdb=" N   ASP A 309 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 306 through 309'
    Processing helix  chain 'A' and resid 310 through 315
      removed outlier: 3.918A  pdb=" N   GLN A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 339
      removed outlier: 3.662A  pdb=" N   MET A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 360
    Processing helix  chain 'A' and resid 378 through 388
    Processing helix  chain 'A' and resid 391 through 401
    Processing helix  chain 'A' and resid 416 through 444
    Processing helix  chain 'A' and resid 472 through 495
    Processing helix  chain 'A' and resid 495 through 504
      removed outlier: 3.503A  pdb=" N   TYR A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 526
      removed outlier: 3.598A  pdb=" N   ILE A 524 " --> pdb=" O   CYS A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 538
      removed outlier: 3.756A  pdb=" N   GLU A 536 " --> pdb=" O   SER A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 557
    Processing helix  chain 'A' and resid 592 through 599
    Processing helix  chain 'A' and resid 602 through 611
    Processing helix  chain 'A' and resid 614 through 621
      removed outlier: 3.595A  pdb=" N   PHE A 621 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 664
      removed outlier: 3.726A  pdb=" N   SER A 664 " --> pdb=" O   THR A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 696
    Processing helix  chain 'A' and resid 697 through 708
      removed outlier: 3.749A  pdb=" N   CYS A 705 " --> pdb=" O   GLY A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 723
    Processing helix  chain 'A' and resid 724 through 726
      No H-bonds generated for 'chain 'A' and resid 724 through 726'
    Processing helix  chain 'A' and resid 737 through 749
      removed outlier: 3.712A  pdb=" N   LYS A 744 " --> pdb=" O   LYS A 740 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   SER A 747 " --> pdb=" O   GLU A 743 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER A 748 " --> pdb=" O   LYS A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 795
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72
      removed outlier: 7.139A  pdb=" N   LYS A  58 " --> pdb=" O   ARG A  54 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   ARG A  54 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   THR A  60 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117
      removed outlier: 6.779A  pdb=" N   CYS A 122 " --> pdb=" O   ARG A 671 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   ILE A 673 " --> pdb=" O   CYS A 122 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   THR A 124 " --> pdb=" O   ILE A 673 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   PHE A 247 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   ILE A 263 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ARG A 249 " --> pdb=" O   ALA A 261 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA A 261 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   HIS A 251 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233
    Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 366
      removed outlier: 6.755A  pdb=" N   LYS A 363 " --> pdb=" O   ASP A 376 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 406
      removed outlier: 3.520A  pdb=" N   GLU A 409 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564
    Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 714

    319 hydrogen bonds defined for protein.
    897 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: 1.98

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1746
        1.33 -     1.46: 1250
        1.46 -     1.58: 3276
        1.58 -     1.70: 3
        1.70 -     1.83: 56
  Bond restraints: 6331
  Sorted by residual:
  bond pdb=" O4  PO4 A1203 "
       pdb=" P   PO4 A1203 "
    ideal  model  delta    sigma   weight residual
    1.568  1.503  0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" O3  PO4 A1203 "
       pdb=" P   PO4 A1203 "
    ideal  model  delta    sigma   weight residual
    1.569  1.508  0.061 2.00e-02 2.50e+03 9.42e+00
  bond pdb=" O2  PO4 A1203 "
       pdb=" P   PO4 A1203 "
    ideal  model  delta    sigma   weight residual
    1.567  1.506  0.061 2.00e-02 2.50e+03 9.34e+00
  bond pdb=" O1  PO4 A1203 "
       pdb=" P   PO4 A1203 "
    ideal  model  delta    sigma   weight residual
    1.565  1.507  0.058 2.00e-02 2.50e+03 8.51e+00
  bond pdb=" C07 XB2 A1204 "
       pdb=" N03 XB2 A1204 "
    ideal  model  delta    sigma   weight residual
    1.425  1.377  0.048 2.00e-02 2.50e+03 5.66e+00
  ... (remaining 6326 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 8184
        2.58 -     5.16: 321
        5.16 -     7.74: 34
        7.74 -    10.32: 0
       10.32 -    12.91: 3
  Bond angle restraints: 8542
  Sorted by residual:
  angle pdb=" C2' ADP A1202 "
        pdb=" C3' ADP A1202 "
        pdb=" C4' ADP A1202 "
      ideal   model   delta    sigma   weight residual
     111.00   98.09   12.91 3.00e+00 1.11e-01 1.85e+01
  angle pdb=" N   LEU A 749 "
        pdb=" CA  LEU A 749 "
        pdb=" C   LEU A 749 "
      ideal   model   delta    sigma   weight residual
     111.71  116.02   -4.31 1.15e+00 7.56e-01 1.41e+01
  angle pdb=" C   TYR A 310 "
        pdb=" N   ALA A 311 "
        pdb=" CA  ALA A 311 "
      ideal   model   delta    sigma   weight residual
     120.54  125.57   -5.03 1.35e+00 5.49e-01 1.39e+01
  angle pdb=" N   GLY A 202 "
        pdb=" CA  GLY A 202 "
        pdb=" C   GLY A 202 "
      ideal   model   delta    sigma   weight residual
     113.30  123.94  -10.64 2.90e+00 1.19e-01 1.35e+01
  angle pdb=" C1' ADP A1202 "
        pdb=" C2' ADP A1202 "
        pdb=" C3' ADP A1202 "
      ideal   model   delta    sigma   weight residual
     111.00  100.36   10.64 3.00e+00 1.11e-01 1.26e+01
  ... (remaining 8537 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.64: 3561
       18.64 -    37.29: 194
       37.29 -    55.93: 38
       55.93 -    74.57: 16
       74.57 -    93.21: 8
  Dihedral angle restraints: 3817
    sinusoidal: 1591
      harmonic: 2226
  Sorted by residual:
  dihedral pdb=" CA  GLN A  44 "
           pdb=" C   GLN A  44 "
           pdb=" N   GLU A  45 "
           pdb=" CA  GLU A  45 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.53  -27.47     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  ALA A 445 "
           pdb=" C   ALA A 445 "
           pdb=" N   THR A 446 "
           pdb=" CA  THR A 446 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.78   27.22     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  GLY A 733 "
           pdb=" C   GLY A 733 "
           pdb=" N   GLN A 734 "
           pdb=" CA  GLN A 734 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.37   25.63     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 3814 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 635
       0.062 -    0.125: 216
       0.125 -    0.187: 59
       0.187 -    0.249: 8
       0.249 -    0.312: 5
  Chirality restraints: 923
  Sorted by residual:
  chirality pdb=" CG  LEU A 749 "
            pdb=" CB  LEU A 749 "
            pdb=" CD1 LEU A 749 "
            pdb=" CD2 LEU A 749 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.28   -0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CB  ILE A  87 "
            pdb=" CA  ILE A  87 "
            pdb=" CG1 ILE A  87 "
            pdb=" CG2 ILE A  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CB  VAL A  39 "
            pdb=" CA  VAL A  39 "
            pdb=" CG1 VAL A  39 "
            pdb=" CG2 VAL A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 920 not shown)

  Planarity restraints: 1099
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C02 XB2 A1204 "   -0.011 2.00e-02 2.50e+03   6.35e-02 1.11e+02
        pdb=" C04 XB2 A1204 "   -0.072 2.00e-02 2.50e+03
        pdb=" C07 XB2 A1204 "    0.009 2.00e-02 2.50e+03
        pdb=" C08 XB2 A1204 "    0.025 2.00e-02 2.50e+03
        pdb=" C09 XB2 A1204 "    0.028 2.00e-02 2.50e+03
        pdb=" C11 XB2 A1204 "   -0.133 2.00e-02 2.50e+03
        pdb=" N03 XB2 A1204 "   -0.021 2.00e-02 2.50e+03
        pdb=" N10 XB2 A1204 "    0.120 2.00e-02 2.50e+03
        pdb=" N19 XB2 A1204 "   -0.031 2.00e-02 2.50e+03
        pdb=" O01 XB2 A1204 "    0.032 2.00e-02 2.50e+03
        pdb=" O20 XB2 A1204 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 567 "    0.344 9.50e-02 1.11e+02   1.57e-01 2.72e+01
        pdb=" NE  ARG A 567 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 567 "   -0.065 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 567 "    0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 567 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 712 "    0.195 9.50e-02 1.11e+02   9.11e-02 1.32e+01
        pdb=" NE  ARG A 712 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 712 "   -0.053 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 712 "    0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 712 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1096 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 71
        2.63 -     3.20: 5428
        3.20 -     3.77: 9418
        3.77 -     4.33: 13855
        4.33 -     4.90: 22781
  Nonbonded interactions: 51553
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 185 "
            pdb="MG    MG A1201 "
     model   vdw
     2.068 2.170
  nonbonded pdb="MG    MG A1201 "
            pdb=" O1  PO4 A1203 "
     model   vdw
     2.098 2.170
  nonbonded pdb="MG    MG A1201 "
            pdb=" O2B ADP A1202 "
     model   vdw
     2.178 2.170
  nonbonded pdb=" OE2 GLU A 535 "
            pdb=" OG  SER A 648 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OG1 THR A 185 "
            pdb=" O2B ADP A1202 "
     model   vdw
     2.340 3.040
  ... (remaining 51548 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 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:             3.300
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.980
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
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      :  0.007   0.077   6331  Z= 0.323
  Angle     :  1.133  12.905   8542  Z= 0.646
  Chirality :  0.070   0.312    923
  Planarity :  0.011   0.157   1099
  Dihedral  : 14.040  93.212   2383
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.36 %
    Favored  : 98.49 %
  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: -1.75 (0.27), residues: 758
  helix: -1.28 (0.22), residues: 372
  sheet: -0.47 (0.60), residues: 57
  loop : -0.94 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 130 
 HIS   0.011   0.003   HIS A 284 
 PHE   0.027   0.003   PHE A 359 
 TYR   0.046   0.007   TYR A 588 
 ARG   0.062   0.007   ARG A 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21674 (  319)
  hydrogen bonds       : angle       8.12801 (  897)
  covalent geometry    : bond        0.00747 ( 6331)
  covalent geometry    : angle       1.13264 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.8023 (mttt) cc_final: 0.7700 (pptt)
REVERT: A  228 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7474 (mp0)
REVERT: A  257 LYS cc_start: 0.7522 (tttt) cc_final: 0.7273 (mmtp)
REVERT: A  365 LYS cc_start: 0.7730 (pttp) cc_final: 0.7490 (ptmm)
REVERT: A  511 ILE cc_start: 0.8030 (mm) cc_final: 0.7721 (mt)
REVERT: A  539 MET cc_start: 0.6102 (mmp) cc_final: 0.5622 (mmm)
REVERT: A  595 GLN cc_start: 0.7300 (mt0) cc_final: 0.7000 (mm110)
REVERT: A  645 GLN cc_start: 0.6392 (tp40) cc_final: 0.5701 (pt0)
REVERT: A  776 MET cc_start: 0.7982 (mtt) cc_final: 0.7711 (mtp)
REVERT: A  780 ARG cc_start: 0.6680 (mtt90) cc_final: 0.6304 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 1.3006
  time to fit residues: 172.9006
Evaluate side-chains
  79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
A  79 GLN
A 104 ASN
A 419 GLN
A 437 ASN
A 555 ASN
A 568 ASN
A 576 HIS
A 581 HIS
A 654 ASN
A 661 ASN
A 668 HIS
A 789 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.159386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.132653 restraints weight = 6890.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.76
r_work: 0.3383 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6331  Z= 0.170
  Angle     :  0.671   8.016   8542  Z= 0.342
  Chirality :  0.046   0.155    923
  Planarity :  0.004   0.043   1099
  Dihedral  :  7.113  96.640    849
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  :  8.45 %
    Favored  : 88.84 %
  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: -0.34 (0.29), residues: 758
  helix:  0.36 (0.26), residues: 377
  sheet: -0.52 (0.61), residues: 57
  loop : -0.77 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 130 
 HIS   0.005   0.001   HIS A 284 
 PHE   0.013   0.001   PHE A 359 
 TYR   0.016   0.002   TYR A 266 
 ARG   0.003   0.000   ARG A 434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04971 (  319)
  hydrogen bonds       : angle       5.35869 (  897)
  covalent geometry    : bond        0.00392 ( 6331)
  covalent geometry    : angle       0.67134 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8183 (t)
REVERT: A   43 LYS cc_start: 0.8287 (mttt) cc_final: 0.7766 (pptt)
REVERT: A  143 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6878 (ttt-90)
REVERT: A  257 LYS cc_start: 0.7841 (tttt) cc_final: 0.7383 (mmtp)
REVERT: A  330 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7676 (mtp)
REVERT: A  374 GLU cc_start: 0.8116 (tt0) cc_final: 0.6938 (tp30)
REVERT: A  403 ARG cc_start: 0.7168 (mtm110) cc_final: 0.6912 (mtm110)
REVERT: A  511 ILE cc_start: 0.8155 (mm) cc_final: 0.7837 (mt)
REVERT: A  539 MET cc_start: 0.7082 (mmp) cc_final: 0.6265 (mmm)
REVERT: A  595 GLN cc_start: 0.7530 (mt0) cc_final: 0.7182 (mm110)
REVERT: A  645 GLN cc_start: 0.6530 (tp40) cc_final: 0.5816 (pt0)
REVERT: A  720 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7022 (pt0)
REVERT: A  776 MET cc_start: 0.8055 (mtt) cc_final: 0.7823 (mtm)
REVERT: A  780 ARG cc_start: 0.6783 (mtt90) cc_final: 0.6418 (mmm160)
REVERT: A  787 ARG cc_start: 0.6759 (mtt-85) cc_final: 0.5823 (ttp-170)
  outliers start: 18
  outliers final: 6
  residues processed: 104
  average time/residue: 1.5132
  time to fit residues: 164.9547
Evaluate side-chains
  88 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  237 ARG
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  685 ASP
Chi-restraints excluded: chain A residue  720 GLN
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  786 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
A 292 ASN
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 676 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.155704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.128265 restraints weight = 7138.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.82
r_work: 0.3375 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6331  Z= 0.206
  Angle     :  0.674   8.123   8542  Z= 0.337
  Chirality :  0.047   0.148    923
  Planarity :  0.004   0.037   1099
  Dihedral  :  6.814  93.556    849
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  :  9.20 %
    Favored  : 87.18 %
  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: -0.31 (0.29), residues: 758
  helix:  0.43 (0.26), residues: 388
  sheet: -0.79 (0.55), residues: 72
  loop : -0.77 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 130 
 HIS   0.006   0.002   HIS A 284 
 PHE   0.017   0.002   PHE A 359 
 TYR   0.016   0.002   TYR A 266 
 ARG   0.003   0.001   ARG A 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04682 (  319)
  hydrogen bonds       : angle       5.16519 (  897)
  covalent geometry    : bond        0.00494 ( 6331)
  covalent geometry    : angle       0.67368 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8236 (t)
REVERT: A   41 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7091 (t0)
REVERT: A   43 LYS cc_start: 0.8361 (mttt) cc_final: 0.7718 (pptt)
REVERT: A  143 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6865 (ttt-90)
REVERT: A  257 LYS cc_start: 0.7869 (tttt) cc_final: 0.7405 (mmtp)
REVERT: A  263 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8657 (mm)
REVERT: A  330 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7699 (mtp)
REVERT: A  374 GLU cc_start: 0.8330 (tt0) cc_final: 0.7015 (tp30)
REVERT: A  418 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6220 (mp10)
REVERT: A  482 ASN cc_start: 0.8326 (m-40) cc_final: 0.8003 (m110)
REVERT: A  511 ILE cc_start: 0.8235 (mm) cc_final: 0.7929 (mt)
REVERT: A  539 MET cc_start: 0.7248 (mmp) cc_final: 0.6453 (mmm)
REVERT: A  595 GLN cc_start: 0.7665 (mt0) cc_final: 0.7254 (mm110)
REVERT: A  645 GLN cc_start: 0.6693 (tp40) cc_final: 0.5798 (pt0)
REVERT: A  720 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7124 (tt0)
REVERT: A  776 MET cc_start: 0.8064 (mtt) cc_final: 0.7861 (mtt)
REVERT: A  780 ARG cc_start: 0.6662 (mtt90) cc_final: 0.6375 (mmm160)
REVERT: A  787 ARG cc_start: 0.6852 (mtt-85) cc_final: 0.5864 (ttp-170)
  outliers start: 24
  outliers final: 6
  residues processed: 102
  average time/residue: 1.2712
  time to fit residues: 135.8773
Evaluate side-chains
  94 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  516 ASP
Chi-restraints excluded: chain A residue  720 GLN
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  786 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 70 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0010
   chunk 38 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.159150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.131744 restraints weight = 7182.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.86
r_work: 0.3418 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6331  Z= 0.126
  Angle     :  0.573   7.846   8542  Z= 0.286
  Chirality :  0.043   0.139    923
  Planarity :  0.003   0.035   1099
  Dihedral  :  6.390  91.697    849
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  :  9.95 %
    Favored  : 86.12 %
  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:  0.08 (0.30), residues: 758
  helix:  0.80 (0.26), residues: 386
  sheet: -0.77 (0.56), residues: 72
  loop : -0.60 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.013   0.001   PHE A 577 
 TYR   0.021   0.001   TYR A 194 
 ARG   0.006   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03775 (  319)
  hydrogen bonds       : angle       4.89478 (  897)
  covalent geometry    : bond        0.00287 ( 6331)
  covalent geometry    : angle       0.57314 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8302 (t)
REVERT: A   43 LYS cc_start: 0.8358 (mttt) cc_final: 0.7708 (pptt)
REVERT: A  143 ARG cc_start: 0.7108 (ttt180) cc_final: 0.6787 (ttt-90)
REVERT: A  194 TYR cc_start: 0.8408 (t80) cc_final: 0.8186 (t80)
REVERT: A  228 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7892 (mp0)
REVERT: A  257 LYS cc_start: 0.7780 (tttt) cc_final: 0.7321 (mmtp)
REVERT: A  366 LEU cc_start: 0.8281 (mt) cc_final: 0.8077 (mt)
REVERT: A  374 GLU cc_start: 0.8287 (tt0) cc_final: 0.7020 (tp30)
REVERT: A  403 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6368 (mtm-85)
REVERT: A  418 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6155 (mp10)
REVERT: A  511 ILE cc_start: 0.8177 (mm) cc_final: 0.7946 (mt)
REVERT: A  539 MET cc_start: 0.7226 (mmp) cc_final: 0.6430 (mmm)
REVERT: A  595 GLN cc_start: 0.7674 (mt0) cc_final: 0.7237 (mm110)
REVERT: A  645 GLN cc_start: 0.6534 (tp40) cc_final: 0.5751 (pt0)
REVERT: A  720 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7179 (tt0)
REVERT: A  776 MET cc_start: 0.8024 (mtt) cc_final: 0.7694 (mtp)
REVERT: A  780 ARG cc_start: 0.6558 (mtt90) cc_final: 0.6271 (mmm160)
REVERT: A  787 ARG cc_start: 0.6851 (mtt-85) cc_final: 0.5879 (ttp-170)
  outliers start: 26
  outliers final: 8
  residues processed: 99
  average time/residue: 1.9256
  time to fit residues: 199.5372
Evaluate side-chains
  90 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  237 ARG
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain A residue  720 GLN
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  786 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 238 ASN
** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 486 GLN
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.157630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.130184 restraints weight = 7134.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.84
r_work: 0.3364 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6331  Z= 0.159
  Angle     :  0.599   7.587   8542  Z= 0.297
  Chirality :  0.044   0.145    923
  Planarity :  0.003   0.037   1099
  Dihedral  :  6.392  92.857    849
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 11.46 %
    Favored  : 84.62 %
  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: -0.03 (0.30), residues: 758
  helix:  0.78 (0.26), residues: 390
  sheet: -0.89 (0.56), residues: 72
  loop : -0.76 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 130 
 HIS   0.004   0.001   HIS A 284 
 PHE   0.014   0.001   PHE A  38 
 TYR   0.014   0.001   TYR A 194 
 ARG   0.005   0.000   ARG A 780 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03993 (  319)
  hydrogen bonds       : angle       4.87755 (  897)
  covalent geometry    : bond        0.00377 ( 6331)
  covalent geometry    : angle       0.59881 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8291 (t)
REVERT: A   43 LYS cc_start: 0.8379 (mttt) cc_final: 0.7738 (ttpt)
REVERT: A  143 ARG cc_start: 0.7175 (ttt180) cc_final: 0.6878 (ttt-90)
REVERT: A  194 TYR cc_start: 0.8483 (t80) cc_final: 0.8260 (t80)
REVERT: A  228 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7957 (mp0)
REVERT: A  257 LYS cc_start: 0.7817 (tttt) cc_final: 0.7363 (mmtp)
REVERT: A  328 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7239 (mt-10)
REVERT: A  363 LYS cc_start: 0.7158 (mmtm) cc_final: 0.6913 (mtpt)
REVERT: A  374 GLU cc_start: 0.8316 (tt0) cc_final: 0.7037 (tp30)
REVERT: A  413 LYS cc_start: 0.7841 (ptpt) cc_final: 0.7190 (ptpp)
REVERT: A  418 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6299 (mp10)
REVERT: A  511 ILE cc_start: 0.8240 (mm) cc_final: 0.8010 (mt)
REVERT: A  539 MET cc_start: 0.7314 (mmp) cc_final: 0.6539 (mmm)
REVERT: A  595 GLN cc_start: 0.7710 (mt0) cc_final: 0.7256 (mm110)
REVERT: A  645 GLN cc_start: 0.6554 (tp40) cc_final: 0.5748 (pt0)
REVERT: A  720 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7238 (tt0)
REVERT: A  787 ARG cc_start: 0.6980 (mtt-85) cc_final: 0.5962 (ttp-170)
  outliers start: 26
  outliers final: 7
  residues processed: 102
  average time/residue: 1.3346
  time to fit residues: 142.3342
Evaluate side-chains
  91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  237 ARG
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  720 GLN
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  786 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 3 optimal weight:    0.4980
   chunk 65 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.159123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.132633 restraints weight = 6994.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.75
r_work: 0.3405 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6331  Z= 0.141
  Angle     :  0.575   8.450   8542  Z= 0.286
  Chirality :  0.043   0.144    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.277  91.870    849
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 12.97 %
    Favored  : 83.71 %
  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:  0.08 (0.30), residues: 758
  helix:  0.87 (0.26), residues: 389
  sheet: -0.97 (0.55), residues: 72
  loop : -0.67 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 112 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.015   0.001   PHE A 359 
 TYR   0.013   0.001   TYR A 266 
 ARG   0.008   0.000   ARG A 780 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03766 (  319)
  hydrogen bonds       : angle       4.83279 (  897)
  covalent geometry    : bond        0.00331 ( 6331)
  covalent geometry    : angle       0.57487 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.649 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8239 (t)
REVERT: A   43 LYS cc_start: 0.8388 (mttt) cc_final: 0.7732 (ttpt)
REVERT: A  143 ARG cc_start: 0.7167 (ttt180) cc_final: 0.6855 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7948 (mp0)
REVERT: A  257 LYS cc_start: 0.7865 (tttt) cc_final: 0.7394 (mmtp)
REVERT: A  328 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7229 (mt-10)
REVERT: A  363 LYS cc_start: 0.7166 (mmtm) cc_final: 0.6936 (mtpt)
REVERT: A  418 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.6350 (mp10)
REVERT: A  511 ILE cc_start: 0.8245 (mm) cc_final: 0.8033 (mt)
REVERT: A  539 MET cc_start: 0.7317 (mmp) cc_final: 0.6537 (mmm)
REVERT: A  595 GLN cc_start: 0.7721 (mt0) cc_final: 0.7288 (mm110)
REVERT: A  720 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7281 (tt0)
REVERT: A  787 ARG cc_start: 0.6878 (mtt-85) cc_final: 0.5947 (ttp-170)
  outliers start: 22
  outliers final: 9
  residues processed: 99
  average time/residue: 1.2942
  time to fit residues: 134.1211
Evaluate side-chains
  89 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  237 ARG
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain A residue  720 GLN
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  786 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 56 optimal weight:    0.0010
   chunk 13 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 676 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.159094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.132562 restraints weight = 7076.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 1.77
r_work: 0.3432 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6331  Z= 0.132
  Angle     :  0.571   8.880   8542  Z= 0.283
  Chirality :  0.042   0.143    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.140  90.213    849
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.48 %
    Favored  : 82.96 %
  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:  0.20 (0.30), residues: 758
  helix:  0.98 (0.26), residues: 391
  sheet: -1.00 (0.55), residues: 72
  loop : -0.63 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.014   0.001   PHE A 577 
 TYR   0.013   0.001   TYR A 266 
 ARG   0.006   0.000   ARG A 780 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03606 (  319)
  hydrogen bonds       : angle       4.78184 (  897)
  covalent geometry    : bond        0.00309 ( 6331)
  covalent geometry    : angle       0.57101 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8233 (t)
REVERT: A   43 LYS cc_start: 0.8415 (mttt) cc_final: 0.7739 (ttpt)
REVERT: A  143 ARG cc_start: 0.7189 (ttt180) cc_final: 0.6895 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7951 (mp0)
REVERT: A  257 LYS cc_start: 0.7867 (tttt) cc_final: 0.7404 (mmtp)
REVERT: A  328 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7240 (mt-10)
REVERT: A  374 GLU cc_start: 0.8178 (tt0) cc_final: 0.7836 (mt-10)
REVERT: A  418 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.6379 (mp10)
REVERT: A  511 ILE cc_start: 0.8261 (mm) cc_final: 0.8048 (mt)
REVERT: A  539 MET cc_start: 0.7333 (mmp) cc_final: 0.6580 (mmm)
REVERT: A  595 GLN cc_start: 0.7747 (mt0) cc_final: 0.7346 (mm110)
REVERT: A  720 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7340 (tt0)
REVERT: A  787 ARG cc_start: 0.6914 (mtt-85) cc_final: 0.5993 (ttp-170)
  outliers start: 17
  outliers final: 8
  residues processed: 97
  average time/residue: 1.5823
  time to fit residues: 160.8413
Evaluate side-chains
  91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  237 ARG
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  720 GLN
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  786 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN
A 676 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.159035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.132448 restraints weight = 7091.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.78
r_work: 0.3403 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6331  Z= 0.139
  Angle     :  0.577  10.482   8542  Z= 0.284
  Chirality :  0.043   0.143    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.121  89.866    849
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.18 %
    Favored  : 82.81 %
  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:  0.26 (0.30), residues: 758
  helix:  1.04 (0.26), residues: 391
  sheet: -1.03 (0.55), residues: 72
  loop : -0.59 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.014   0.001   PHE A 359 
 TYR   0.013   0.001   TYR A 266 
 ARG   0.008   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03621 (  319)
  hydrogen bonds       : angle       4.76415 (  897)
  covalent geometry    : bond        0.00325 ( 6331)
  covalent geometry    : angle       0.57732 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 1.659 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8250 (t)
REVERT: A   43 LYS cc_start: 0.8405 (mttt) cc_final: 0.7690 (ttpt)
REVERT: A  143 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6889 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7950 (mp0)
REVERT: A  257 LYS cc_start: 0.7772 (tttt) cc_final: 0.7321 (mmtp)
REVERT: A  328 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7224 (mt-10)
REVERT: A  374 GLU cc_start: 0.8181 (tt0) cc_final: 0.7804 (mt-10)
REVERT: A  418 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6430 (mp10)
REVERT: A  511 ILE cc_start: 0.8254 (mm) cc_final: 0.8049 (mt)
REVERT: A  539 MET cc_start: 0.7308 (mmp) cc_final: 0.6553 (mmm)
REVERT: A  554 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7254 (m-30)
REVERT: A  595 GLN cc_start: 0.7741 (mt0) cc_final: 0.7307 (mm110)
REVERT: A  720 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7330 (tt0)
REVERT: A  787 ARG cc_start: 0.6845 (mtt-85) cc_final: 0.5947 (ttp-170)
  outliers start: 20
  outliers final: 9
  residues processed: 94
  average time/residue: 1.3610
  time to fit residues: 135.5442
Evaluate side-chains
  88 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  237 ARG
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  554 ASP
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain A residue  720 GLN
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  786 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN
A 676 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.158500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131789 restraints weight = 7128.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.78
r_work: 0.3392 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6331  Z= 0.151
  Angle     :  0.591  11.054   8542  Z= 0.290
  Chirality :  0.043   0.142    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.157  90.489    849
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.78 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.20 (0.30), residues: 758
  helix:  0.99 (0.26), residues: 392
  sheet: -1.01 (0.55), residues: 72
  loop : -0.63 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 112 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.014   0.001   PHE A 359 
 TYR   0.013   0.001   TYR A 266 
 ARG   0.007   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03713 (  319)
  hydrogen bonds       : angle       4.76165 (  897)
  covalent geometry    : bond        0.00359 ( 6331)
  covalent geometry    : angle       0.59092 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8275 (t)
REVERT: A   43 LYS cc_start: 0.8397 (mttt) cc_final: 0.7680 (ttpt)
REVERT: A  143 ARG cc_start: 0.7179 (ttt180) cc_final: 0.6880 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7963 (mp0)
REVERT: A  257 LYS cc_start: 0.7861 (tttt) cc_final: 0.7418 (mmtp)
REVERT: A  328 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7266 (mt-10)
REVERT: A  374 GLU cc_start: 0.8200 (tt0) cc_final: 0.7826 (mt-10)
REVERT: A  418 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6390 (mp10)
REVERT: A  482 ASN cc_start: 0.8242 (m-40) cc_final: 0.7960 (m110)
REVERT: A  511 ILE cc_start: 0.8257 (mm) cc_final: 0.8050 (mt)
REVERT: A  539 MET cc_start: 0.7319 (mmp) cc_final: 0.6556 (mmm)
REVERT: A  554 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7323 (m-30)
REVERT: A  595 GLN cc_start: 0.7757 (mt0) cc_final: 0.7319 (mm110)
REVERT: A  720 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7347 (tt0)
REVERT: A  787 ARG cc_start: 0.6852 (mtt-85) cc_final: 0.5948 (ttp-170)
  outliers start: 17
  outliers final: 9
  residues processed: 91
  average time/residue: 1.3626
  time to fit residues: 130.2739
Evaluate side-chains
  90 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  237 ARG
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  554 ASP
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain A residue  720 GLN
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  786 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.158918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.132088 restraints weight = 7156.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.79
r_work: 0.3399 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6331  Z= 0.144
  Angle     :  0.591  11.380   8542  Z= 0.289
  Chirality :  0.043   0.142    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.135  90.039    849
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.78 %
    Favored  : 82.96 %
  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:  0.23 (0.30), residues: 758
  helix:  1.01 (0.27), residues: 392
  sheet: -1.00 (0.56), residues: 72
  loop : -0.61 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.013   0.001   PHE A 577 
 TYR   0.013   0.001   TYR A 266 
 ARG   0.007   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03662 (  319)
  hydrogen bonds       : angle       4.73891 (  897)
  covalent geometry    : bond        0.00341 ( 6331)
  covalent geometry    : angle       0.59128 ( 8542)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.8327 (mttt) cc_final: 0.7659 (ttpt)
REVERT: A  143 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6874 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7956 (mp0)
REVERT: A  257 LYS cc_start: 0.7885 (tttt) cc_final: 0.7433 (mmtp)
REVERT: A  328 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7269 (mt-10)
REVERT: A  374 GLU cc_start: 0.8190 (tt0) cc_final: 0.7810 (mt-10)
REVERT: A  418 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6389 (mp10)
REVERT: A  482 ASN cc_start: 0.8258 (m-40) cc_final: 0.7971 (m110)
REVERT: A  511 ILE cc_start: 0.8266 (mm) cc_final: 0.8063 (mt)
REVERT: A  539 MET cc_start: 0.7324 (mmp) cc_final: 0.6572 (mmm)
REVERT: A  554 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7326 (m-30)
REVERT: A  595 GLN cc_start: 0.7756 (mt0) cc_final: 0.7309 (mm110)
REVERT: A  720 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7331 (tt0)
REVERT: A  787 ARG cc_start: 0.6807 (mtt-85) cc_final: 0.5931 (ttp-170)
  outliers start: 15
  outliers final: 9
  residues processed: 89
  average time/residue: 1.5247
  time to fit residues: 142.3746
Evaluate side-chains
  92 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  237 ARG
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  554 ASP
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain A residue  720 GLN
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  786 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 15 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    0.3980
   chunk 27 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.159747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.133131 restraints weight = 7158.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.77
r_work: 0.3436 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6331  Z= 0.130
  Angle     :  0.579  11.898   8542  Z= 0.283
  Chirality :  0.042   0.140    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.042  87.982    849
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.63 %
    Favored  : 82.81 %
  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:  0.33 (0.31), residues: 758
  helix:  1.10 (0.27), residues: 390
  sheet: -1.00 (0.56), residues: 72
  loop : -0.55 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 130 
 HIS   0.002   0.001   HIS A  97 
 PHE   0.014   0.001   PHE A 577 
 TYR   0.012   0.001   TYR A 266 
 ARG   0.008   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  319)
  hydrogen bonds       : angle       4.69108 (  897)
  covalent geometry    : bond        0.00304 ( 6331)
  covalent geometry    : angle       0.57908 ( 8542)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5602.87 seconds
wall clock time: 99 minutes 40.14 seconds (5980.14 seconds total)