Starting phenix.real_space_refine
on Sat May 10 12:19:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gz2_51720/05_2025/9gz2_51720.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gz2_51720/05_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_51720/05_2025/9gz2_51720.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gz2_51720/05_2025/9gz2_51720.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gz2_51720/05_2025/9gz2_51720.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gz2_51720/05_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.31, per 1000 atoms: 0.86
  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: 1.77
  Conformation dependent library (CDL) restraints added in 931.1 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: 0.76
  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: 2.02

  Time building geometry restraints manager: 1.95 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:             3.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.890
  Find NCS groups from input model:        0.060
  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:12.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.160
-------------------------------------------------------------------------------
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  : 0.685 
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: 1.2637
  time to fit residues: 167.9293
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  : 0.726 
-------------------------------------------------------------------------------
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 = 36)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.132735 restraints weight = 6890.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.74
r_work: 0.3386 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
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  : 0.764 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8184 (t)
REVERT: A   43 LYS cc_start: 0.8281 (mttt) cc_final: 0.7762 (pptt)
REVERT: A  143 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6877 (ttt-90)
REVERT: A  257 LYS cc_start: 0.7841 (tttt) cc_final: 0.7393 (mmtp)
REVERT: A  330 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7672 (mtp)
REVERT: A  374 GLU cc_start: 0.8112 (tt0) cc_final: 0.6926 (tp30)
REVERT: A  403 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6907 (mtm110)
REVERT: A  511 ILE cc_start: 0.8160 (mm) cc_final: 0.7841 (mt)
REVERT: A  539 MET cc_start: 0.7076 (mmp) cc_final: 0.6258 (mmm)
REVERT: A  595 GLN cc_start: 0.7529 (mt0) cc_final: 0.7171 (mm110)
REVERT: A  645 GLN cc_start: 0.6523 (tp40) cc_final: 0.5811 (pt0)
REVERT: A  720 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7012 (pt0)
REVERT: A  776 MET cc_start: 0.8045 (mtt) cc_final: 0.7811 (mtm)
REVERT: A  780 ARG cc_start: 0.6776 (mtt90) cc_final: 0.6407 (mmm160)
REVERT: A  787 ARG cc_start: 0.6741 (mtt-85) cc_final: 0.5813 (ttp-170)
  outliers start: 18
  outliers final: 6
  residues processed: 104
  average time/residue: 1.3604
  time to fit residues: 148.1347
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  : 0.736 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.157706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.130425 restraints weight = 7128.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.84
r_work: 0.3374 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2242

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= 0.166
  Angle     :  0.630   7.972   8542  Z= 0.316
  Chirality :  0.045   0.142    923
  Planarity :  0.004   0.036   1099
  Dihedral  :  6.641  92.514    849
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  :  9.05 %
    Favored  : 87.33 %
  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: -0.07 (0.30), residues: 758
  helix:  0.64 (0.26), residues: 384
  sheet: -0.71 (0.56), residues: 72
  loop : -0.64 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 130 
 HIS   0.005   0.001   HIS A 284 
 PHE   0.015   0.001   PHE A 359 
 TYR   0.014   0.002   TYR A 266 
 ARG   0.002   0.000   ARG A 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04384 (  319)
  hydrogen bonds       : angle       5.07765 (  897)
  covalent geometry    : bond        0.00390 ( 6331)
  covalent geometry    : angle       0.63038 ( 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
  109 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8217 (t)
REVERT: A   43 LYS cc_start: 0.8347 (mttt) cc_final: 0.7763 (pptt)
REVERT: A  143 ARG cc_start: 0.7161 (ttt180) cc_final: 0.6845 (ttt-90)
REVERT: A  257 LYS cc_start: 0.7811 (tttt) cc_final: 0.7388 (mmtp)
REVERT: A  263 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8613 (mm)
REVERT: A  330 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7679 (mtp)
REVERT: A  374 GLU cc_start: 0.8272 (tt0) cc_final: 0.7005 (tp30)
REVERT: A  418 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6283 (mp10)
REVERT: A  482 ASN cc_start: 0.8288 (m-40) cc_final: 0.7989 (m110)
REVERT: A  511 ILE cc_start: 0.8224 (mm) cc_final: 0.7909 (mt)
REVERT: A  539 MET cc_start: 0.7236 (mmp) cc_final: 0.6463 (mmm)
REVERT: A  595 GLN cc_start: 0.7637 (mt0) cc_final: 0.7226 (mm110)
REVERT: A  645 GLN cc_start: 0.6564 (tp40) cc_final: 0.5828 (pt0)
REVERT: A  720 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7146 (tt0)
REVERT: A  776 MET cc_start: 0.8068 (mtt) cc_final: 0.7859 (mtt)
REVERT: A  780 ARG cc_start: 0.6674 (mtt90) cc_final: 0.6413 (mmm160)
REVERT: A  787 ARG cc_start: 0.6885 (mtt-85) cc_final: 0.5901 (ttp-170)
  outliers start: 24
  outliers final: 7
  residues processed: 98
  average time/residue: 1.3968
  time to fit residues: 143.1734
Evaluate side-chains
  90 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
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   60 THR
Chi-restraints excluded: chain A residue  237 ARG
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  521 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0570
   chunk 38 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
A 238 ASN
** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3853 r_free = 0.3853 target = 0.158711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.131352 restraints weight = 7178.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.85
r_work: 0.3413 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2478

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= 0.135
  Angle     :  0.581   8.030   8542  Z= 0.289
  Chirality :  0.043   0.138    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.378  91.417    849
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 10.11 %
    Favored  : 85.82 %
  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:  0.10 (0.30), residues: 758
  helix:  0.83 (0.26), residues: 386
  sheet: -0.76 (0.56), residues: 72
  loop : -0.61 (0.36), residues: 300

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   0.012   0.001   PHE A 577 
 TYR   0.020   0.001   TYR A 194 
 ARG   0.006   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  319)
  hydrogen bonds       : angle       4.87910 (  897)
  covalent geometry    : bond        0.00311 ( 6331)
  covalent geometry    : angle       0.58055 ( 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
  108 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8304 (t)
REVERT: A   43 LYS cc_start: 0.8357 (mttt) cc_final: 0.7711 (pptt)
REVERT: A  143 ARG cc_start: 0.7138 (ttt180) cc_final: 0.6811 (ttt-90)
REVERT: A  194 TYR cc_start: 0.8411 (t80) cc_final: 0.8182 (t80)
REVERT: A  228 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7897 (mp0)
REVERT: A  257 LYS cc_start: 0.7785 (tttt) cc_final: 0.7320 (mmtp)
REVERT: A  263 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8626 (mm)
REVERT: A  366 LEU cc_start: 0.8319 (mt) cc_final: 0.8114 (mt)
REVERT: A  374 GLU cc_start: 0.8313 (tt0) cc_final: 0.7028 (tp30)
REVERT: A  418 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.6182 (mp10)
REVERT: A  511 ILE cc_start: 0.8174 (mm) cc_final: 0.7870 (mt)
REVERT: A  539 MET cc_start: 0.7243 (mmp) cc_final: 0.6458 (mmm)
REVERT: A  595 GLN cc_start: 0.7676 (mt0) cc_final: 0.7250 (mm110)
REVERT: A  645 GLN cc_start: 0.6479 (tp40) cc_final: 0.5774 (pt0)
REVERT: A  720 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7190 (tt0)
REVERT: A  776 MET cc_start: 0.8032 (mtt) cc_final: 0.7703 (mtp)
REVERT: A  780 ARG cc_start: 0.6504 (mtt90) cc_final: 0.6233 (mmm160)
REVERT: A  787 ARG cc_start: 0.6878 (mtt-85) cc_final: 0.5871 (ttp-170)
  outliers start: 27
  outliers final: 10
  residues processed: 95
  average time/residue: 1.4321
  time to fit residues: 142.0665
Evaluate side-chains
  92 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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  113 MET
Chi-restraints excluded: chain A residue  237 ARG
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  521 ILE
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:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0870
   chunk 54 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0570
   chunk 74 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0870
   chunk 59 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.3254

-------------------------------------------------------------------------------
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 = 0.3875 r_free = 0.3875 target = 0.160756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.133630 restraints weight = 7098.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.84
r_work: 0.3435 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6331  Z= 0.111
  Angle     :  0.552   8.448   8542  Z= 0.274
  Chirality :  0.042   0.134    923
  Planarity :  0.003   0.035   1099
  Dihedral  :  6.151  88.970    849
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 10.56 %
    Favored  : 85.82 %
  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:  0.25 (0.30), residues: 758
  helix:  1.02 (0.26), residues: 387
  sheet: -0.84 (0.56), residues: 72
  loop : -0.60 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 556 
 PHE   0.012   0.001   PHE A 577 
 TYR   0.012   0.001   TYR A 194 
 ARG   0.004   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03571 (  319)
  hydrogen bonds       : angle       4.78694 (  897)
  covalent geometry    : bond        0.00246 ( 6331)
  covalent geometry    : angle       0.55217 ( 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
  112 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8260 (t)
REVERT: A   43 LYS cc_start: 0.8369 (mttt) cc_final: 0.7681 (pptt)
REVERT: A  143 ARG cc_start: 0.7120 (ttt180) cc_final: 0.6784 (ttt-90)
REVERT: A  194 TYR cc_start: 0.8408 (t80) cc_final: 0.8206 (t80)
REVERT: A  228 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7824 (mp0)
REVERT: A  257 LYS cc_start: 0.7747 (tttt) cc_final: 0.7301 (mmtp)
REVERT: A  263 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8614 (mm)
REVERT: A  328 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7121 (mt-10)
REVERT: A  363 LYS cc_start: 0.7110 (mmtm) cc_final: 0.6857 (mtpt)
REVERT: A  374 GLU cc_start: 0.8284 (tt0) cc_final: 0.7021 (tp30)
REVERT: A  403 ARG cc_start: 0.7322 (mtm110) cc_final: 0.6435 (mtm-85)
REVERT: A  418 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.6221 (mp10)
REVERT: A  511 ILE cc_start: 0.8180 (mm) cc_final: 0.7864 (mt)
REVERT: A  539 MET cc_start: 0.7251 (mmp) cc_final: 0.6493 (mmm)
REVERT: A  595 GLN cc_start: 0.7663 (mt0) cc_final: 0.7219 (mm110)
REVERT: A  645 GLN cc_start: 0.6225 (tp40) cc_final: 0.5591 (pt0)
REVERT: A  720 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7226 (tt0)
REVERT: A  776 MET cc_start: 0.7977 (mtt) cc_final: 0.7691 (mtp)
REVERT: A  787 ARG cc_start: 0.6849 (mtt-85) cc_final: 0.5883 (ttp-170)
  outliers start: 24
  outliers final: 9
  residues processed: 100
  average time/residue: 1.2729
  time to fit residues: 133.6383
Evaluate side-chains
  92 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
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  263 ILE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  521 ILE
Chi-restraints excluded: chain A residue  546 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 65 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
A  75 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 187 ASN
A 238 ASN
A 486 GLN
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 676 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.158953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.132434 restraints weight = 7029.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.76
r_work: 0.3436 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6331  Z= 0.154
  Angle     :  0.590   8.592   8542  Z= 0.292
  Chirality :  0.044   0.144    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.263  91.844    849
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 11.46 %
    Favored  : 84.92 %
  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:  0.14 (0.30), residues: 758
  helix:  0.88 (0.26), residues: 389
  sheet: -0.86 (0.56), residues: 72
  loop : -0.60 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 112 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.014   0.001   PHE A  38 
 TYR   0.013   0.001   TYR A 266 
 ARG   0.003   0.000   ARG A 723 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  319)
  hydrogen bonds       : angle       4.81491 (  897)
  covalent geometry    : bond        0.00364 ( 6331)
  covalent geometry    : angle       0.58995 ( 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
  109 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8189 (t)
REVERT: A   43 LYS cc_start: 0.8374 (mttt) cc_final: 0.7769 (ttpt)
REVERT: A  143 ARG cc_start: 0.7177 (ttt180) cc_final: 0.6882 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7986 (mp0)
REVERT: A  257 LYS cc_start: 0.7809 (tttt) cc_final: 0.7403 (mmtp)
REVERT: A  263 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8623 (mm)
REVERT: A  328 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7266 (mt-10)
REVERT: A  374 GLU cc_start: 0.8317 (tt0) cc_final: 0.7055 (tp30)
REVERT: A  418 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.6386 (mp10)
REVERT: A  482 ASN cc_start: 0.8258 (m-40) cc_final: 0.7977 (m110)
REVERT: A  511 ILE cc_start: 0.8280 (mm) cc_final: 0.7965 (mt)
REVERT: A  539 MET cc_start: 0.7327 (mmp) cc_final: 0.6558 (mmm)
REVERT: A  554 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7287 (m-30)
REVERT: A  595 GLN cc_start: 0.7753 (mt0) cc_final: 0.7347 (mm110)
REVERT: A  645 GLN cc_start: 0.6440 (tp40) cc_final: 0.5755 (pt0)
REVERT: A  720 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7321 (tt0)
REVERT: A  776 MET cc_start: 0.8139 (mtt) cc_final: 0.7822 (mtp)
REVERT: A  787 ARG cc_start: 0.6915 (mtt-85) cc_final: 0.5989 (ttp-170)
  outliers start: 24
  outliers final: 8
  residues processed: 98
  average time/residue: 1.3277
  time to fit residues: 136.2127
Evaluate side-chains
  91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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  263 ILE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  546 MET
Chi-restraints excluded: chain A residue  554 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:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 75 optimal weight:    0.4980
   chunk 1 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 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 = 0.3839 r_free = 0.3839 target = 0.157696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.130129 restraints weight = 7132.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.86
r_work: 0.3392 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2900

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= 0.146
  Angle     :  0.586   9.012   8542  Z= 0.290
  Chirality :  0.043   0.140    923
  Planarity :  0.003   0.035   1099
  Dihedral  :  6.277  94.375    849
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 12.37 %
    Favored  : 84.31 %
  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:  0.17 (0.30), residues: 758
  helix:  0.95 (0.26), residues: 389
  sheet: -0.93 (0.55), residues: 72
  loop : -0.64 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   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   0.010   0.001   ARG A 780 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  319)
  hydrogen bonds       : angle       4.79094 (  897)
  covalent geometry    : bond        0.00345 ( 6331)
  covalent geometry    : angle       0.58610 ( 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
  104 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8263 (t)
REVERT: A   43 LYS cc_start: 0.8409 (mttt) cc_final: 0.7715 (ttpt)
REVERT: A  143 ARG cc_start: 0.7148 (ttt180) cc_final: 0.6842 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7948 (mp0)
REVERT: A  257 LYS cc_start: 0.7891 (tttt) cc_final: 0.7425 (mmtp)
REVERT: A  263 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8638 (mm)
REVERT: A  328 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7199 (mt-10)
REVERT: A  418 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6367 (mp10)
REVERT: A  482 ASN cc_start: 0.8264 (m-40) cc_final: 0.7970 (m110)
REVERT: A  497 GLU cc_start: 0.8256 (tp30) cc_final: 0.7974 (tp30)
REVERT: A  511 ILE cc_start: 0.8237 (mm) cc_final: 0.8019 (mt)
REVERT: A  539 MET cc_start: 0.7321 (mmp) cc_final: 0.6548 (mmm)
REVERT: A  595 GLN cc_start: 0.7717 (mt0) cc_final: 0.7265 (mm110)
REVERT: A  720 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7296 (tt0)
REVERT: A  740 LYS cc_start: 0.8051 (pttp) cc_final: 0.7730 (pptt)
REVERT: A  776 MET cc_start: 0.8041 (mtt) cc_final: 0.7738 (mtp)
REVERT: A  787 ARG cc_start: 0.6870 (mtt-85) cc_final: 0.5924 (ttp-170)
  outliers start: 22
  outliers final: 8
  residues processed: 95
  average time/residue: 1.3400
  time to fit residues: 133.3836
Evaluate side-chains
  91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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  263 ILE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  546 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 58 optimal weight:    0.0570
   chunk 42 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5098

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.160035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.133416 restraints weight = 7057.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.79
r_work: 0.3416 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6331  Z= 0.124
  Angle     :  0.566  10.188   8542  Z= 0.279
  Chirality :  0.042   0.141    923
  Planarity :  0.003   0.035   1099
  Dihedral  :  6.150  93.239    849
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.97 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.30), residues: 758
  helix:  1.08 (0.26), residues: 389
  sheet: -0.91 (0.57), residues: 72
  loop : -0.56 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 130 
 HIS   0.002   0.001   HIS A 556 
 PHE   0.013   0.001   PHE A 577 
 TYR   0.012   0.001   TYR A 266 
 ARG   0.009   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  319)
  hydrogen bonds       : angle       4.69024 (  897)
  covalent geometry    : bond        0.00288 ( 6331)
  covalent geometry    : angle       0.56580 ( 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
  100 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8275 (t)
REVERT: A   43 LYS cc_start: 0.8416 (mttt) cc_final: 0.7696 (ttpt)
REVERT: A  143 ARG cc_start: 0.7168 (ttt180) cc_final: 0.6860 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7934 (mp0)
REVERT: A  257 LYS cc_start: 0.7786 (tttt) cc_final: 0.7343 (mmtp)
REVERT: A  263 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8626 (mm)
REVERT: A  328 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7203 (mt-10)
REVERT: A  418 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.6384 (mp10)
REVERT: A  497 GLU cc_start: 0.8182 (tp30) cc_final: 0.7968 (tp30)
REVERT: A  511 ILE cc_start: 0.8251 (mm) cc_final: 0.8038 (mt)
REVERT: A  539 MET cc_start: 0.7329 (mmp) cc_final: 0.6563 (mmm)
REVERT: A  595 GLN cc_start: 0.7701 (mt0) cc_final: 0.7278 (mm110)
REVERT: A  645 GLN cc_start: 0.6537 (tp-100) cc_final: 0.5434 (pt0)
REVERT: A  720 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7319 (tt0)
REVERT: A  740 LYS cc_start: 0.7966 (pttp) cc_final: 0.7622 (pptt)
REVERT: A  776 MET cc_start: 0.8029 (mtt) cc_final: 0.7753 (mtp)
REVERT: A  787 ARG cc_start: 0.6816 (mtt-85) cc_final: 0.5936 (ttp-170)
  outliers start: 21
  outliers final: 9
  residues processed: 91
  average time/residue: 1.3717
  time to fit residues: 130.6109
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  : 0.676 
-------------------------------------------------------------------------------
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  263 ILE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  521 ILE
Chi-restraints excluded: chain A residue  546 MET
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain A residue  720 GLN
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:    0.2980
   chunk 66 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0020
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0770
   chunk 20 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 39 optimal weight:    8.9990
   overall best weight:    0.3346

-------------------------------------------------------------------------------
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 = 0.3881 r_free = 0.3881 target = 0.161626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.135081 restraints weight = 7119.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.78
r_work: 0.3438 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6331  Z= 0.106
  Angle     :  0.546  10.742   8542  Z= 0.269
  Chirality :  0.041   0.138    923
  Planarity :  0.003   0.035   1099
  Dihedral  :  5.970  89.993    849
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.12 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.30), residues: 758
  helix:  1.22 (0.27), residues: 391
  sheet: -0.93 (0.57), residues: 72
  loop : -0.50 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 556 
 PHE   0.013   0.001   PHE A 577 
 TYR   0.010   0.001   TYR A 266 
 ARG   0.007   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03285 (  319)
  hydrogen bonds       : angle       4.55792 (  897)
  covalent geometry    : bond        0.00239 ( 6331)
  covalent geometry    : angle       0.54634 ( 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
  106 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.736 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.8389 (mttt) cc_final: 0.7687 (ttpt)
REVERT: A  143 ARG cc_start: 0.7200 (ttt180) cc_final: 0.6865 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7874 (mp0)
REVERT: A  257 LYS cc_start: 0.7758 (tttt) cc_final: 0.7308 (mmtp)
REVERT: A  263 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8601 (mm)
REVERT: A  328 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7192 (mt-10)
REVERT: A  511 ILE cc_start: 0.8240 (mm) cc_final: 0.8023 (mt)
REVERT: A  539 MET cc_start: 0.7288 (mmp) cc_final: 0.6515 (mmm)
REVERT: A  554 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7284 (m-30)
REVERT: A  595 GLN cc_start: 0.7665 (mt0) cc_final: 0.7242 (mm110)
REVERT: A  645 GLN cc_start: 0.6507 (tp-100) cc_final: 0.5575 (pt0)
REVERT: A  720 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7331 (tt0)
REVERT: A  740 LYS cc_start: 0.7869 (pttp) cc_final: 0.7509 (pptt)
REVERT: A  776 MET cc_start: 0.7998 (mtt) cc_final: 0.7743 (mtp)
REVERT: A  787 ARG cc_start: 0.6821 (mtt-85) cc_final: 0.5954 (ttp-170)
  outliers start: 20
  outliers final: 7
  residues processed: 97
  average time/residue: 1.3856
  time to fit residues: 140.9203
Evaluate side-chains
  92 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
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  263 ILE
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  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:    0.7980
   chunk 36 optimal weight:    0.3980
   chunk 75 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 49 optimal weight:    0.3980
   chunk 29 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0980
   chunk 45 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.3780

-------------------------------------------------------------------------------
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 126 ASN
** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.161743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.135200 restraints weight = 7167.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.80
r_work: 0.3436 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3258

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= 0.114
  Angle     :  0.573  11.859   8542  Z= 0.281
  Chirality :  0.041   0.139    923
  Planarity :  0.003   0.035   1099
  Dihedral  :  5.906  87.802    849
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.78 %
    Favored  : 83.56 %
  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:  0.51 (0.31), residues: 758
  helix:  1.28 (0.27), residues: 390
  sheet: -0.95 (0.57), residues: 72
  loop : -0.49 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 556 
 PHE   0.013   0.001   PHE A 577 
 TYR   0.011   0.001   TYR A 266 
 ARG   0.007   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  319)
  hydrogen bonds       : angle       4.53584 (  897)
  covalent geometry    : bond        0.00260 ( 6331)
  covalent geometry    : angle       0.57330 ( 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
  97 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.8348 (mttt) cc_final: 0.7655 (ttpt)
REVERT: A  143 ARG cc_start: 0.7205 (ttt180) cc_final: 0.6853 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7880 (mp0)
REVERT: A  257 LYS cc_start: 0.7778 (tttt) cc_final: 0.7378 (mmtp)
REVERT: A  263 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8606 (mm)
REVERT: A  328 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7205 (mt-10)
REVERT: A  374 GLU cc_start: 0.8149 (tt0) cc_final: 0.7788 (mt-10)
REVERT: A  511 ILE cc_start: 0.8256 (mm) cc_final: 0.7941 (mt)
REVERT: A  539 MET cc_start: 0.7225 (mmp) cc_final: 0.6468 (mmm)
REVERT: A  554 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7292 (m-30)
REVERT: A  595 GLN cc_start: 0.7632 (mt0) cc_final: 0.7222 (mm110)
REVERT: A  645 GLN cc_start: 0.6499 (tp-100) cc_final: 0.5579 (pt0)
REVERT: A  720 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7338 (tt0)
REVERT: A  740 LYS cc_start: 0.7830 (pttp) cc_final: 0.7501 (pptt)
REVERT: A  776 MET cc_start: 0.7960 (mtt) cc_final: 0.7699 (mtp)
REVERT: A  787 ARG cc_start: 0.6767 (mtt-85) cc_final: 0.5951 (ttp-170)
  outliers start: 11
  outliers final: 6
  residues processed: 92
  average time/residue: 1.2921
  time to fit residues: 124.6105
Evaluate side-chains
  92 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
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  263 ILE
Chi-restraints excluded: chain A residue  554 ASP
Chi-restraints excluded: chain A residue  720 GLN
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:    0.1980
   chunk 9 optimal weight:    0.0270
   chunk 38 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 4 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 20 optimal weight:    0.4980
   chunk 66 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0670
   overall best weight:    0.2176

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
A  75 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 GLN
** A 416 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 = 0.3906 r_free = 0.3906 target = 0.163623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.137529 restraints weight = 7160.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.79
r_work: 0.3467 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6331  Z= 0.100
  Angle     :  0.547  11.276   8542  Z= 0.267
  Chirality :  0.041   0.137    923
  Planarity :  0.003   0.035   1099
  Dihedral  :  5.705  78.572    849
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.93 %
    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:  0.65 (0.31), residues: 758
  helix:  1.43 (0.27), residues: 389
  sheet: -0.94 (0.57), residues: 72
  loop : -0.48 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 556 
 PHE   0.013   0.001   PHE A 577 
 TYR   0.009   0.001   TYR A 266 
 ARG   0.008   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03094 (  319)
  hydrogen bonds       : angle       4.43421 (  897)
  covalent geometry    : bond        0.00220 ( 6331)
  covalent geometry    : angle       0.54706 ( 8542)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5005.59 seconds
wall clock time: 87 minutes 11.12 seconds (5231.12 seconds total)