Starting phenix.real_space_refine
on Wed Sep 17 06:36:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gz2_51720/09_2025/9gz2_51720.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gz2_51720/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gz2_51720/09_2025/9gz2_51720.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gz2_51720/09_2025/9gz2_51720.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gz2_51720/09_2025/9gz2_51720.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gz2_51720/09_2025/9gz2_51720.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.80, per 1000 atoms: 0.29
  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: 0.51
  Conformation dependent library (CDL) restraints added in 404.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.23
  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: 1.15

  Time building geometry restraints manager: 0.69 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:             3.800
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.220
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.130
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.062   0.007   ARG A 567 
 TYR   0.046   0.007   TYR A 588 
 PHE   0.027   0.003   PHE A 359 
 TRP   0.019   0.002   TRP A 130 
 HIS   0.011   0.003   HIS A 284 

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

*********************** 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  : 0.247 
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: 0.6073
  time to fit residues: 80.4382
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  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   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 = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.132551 restraints weight = 7042.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.78
r_work: 0.3405 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (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
 ARG   0.003   0.000   ARG A 434 
 TYR   0.016   0.002   TYR A 266 
 PHE   0.013   0.001   PHE A 359 
 TRP   0.010   0.001   TRP A 130 
 HIS   0.005   0.001   HIS A 284 

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

*********************** 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  : 0.234 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8203 (t)
REVERT: A   43 LYS cc_start: 0.8310 (mttt) cc_final: 0.7766 (pptt)
REVERT: A  143 ARG cc_start: 0.7140 (ttt180) cc_final: 0.6888 (ttt-90)
REVERT: A  257 LYS cc_start: 0.7853 (tttt) cc_final: 0.7392 (mmtp)
REVERT: A  330 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7683 (mtp)
REVERT: A  374 GLU cc_start: 0.8119 (tt0) cc_final: 0.6930 (tp30)
REVERT: A  403 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6903 (mtm110)
REVERT: A  511 ILE cc_start: 0.8152 (mm) cc_final: 0.7837 (mt)
REVERT: A  539 MET cc_start: 0.7114 (mmp) cc_final: 0.6288 (mmm)
REVERT: A  595 GLN cc_start: 0.7535 (mt0) cc_final: 0.7175 (mm110)
REVERT: A  645 GLN cc_start: 0.6547 (tp40) cc_final: 0.5812 (pt0)
REVERT: A  720 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7022 (pt0)
REVERT: A  776 MET cc_start: 0.8038 (mtt) cc_final: 0.7803 (mtm)
REVERT: A  780 ARG cc_start: 0.6756 (mtt90) cc_final: 0.6381 (mmm160)
REVERT: A  787 ARG cc_start: 0.6719 (mtt-85) cc_final: 0.5772 (ttp-170)
  outliers start: 18
  outliers final: 6
  residues processed: 104
  average time/residue: 0.5894
  time to fit residues: 63.9861
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  : 0.158 
-------------------------------------------------------------------------------
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 17 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    0.2980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 288 GLN
** 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 = 0.3806 r_free = 0.3806 target = 0.154363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.126902 restraints weight = 7125.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.81
r_work: 0.3358 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
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      :  0.006   0.057   6331  Z= 0.244
  Angle     :  0.712   8.100   8542  Z= 0.356
  Chirality :  0.049   0.154    923
  Planarity :  0.004   0.039   1099
  Dihedral  :  6.951  94.479    849
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  :  9.50 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.29), residues: 758
  helix:  0.30 (0.26), residues: 388
  sheet: -0.86 (0.56), residues: 72
  loop : -0.83 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 567 
 TYR   0.017   0.002   TYR A 266 
 PHE   0.018   0.002   PHE A 359 
 TRP   0.009   0.002   TRP A 130 
 HIS   0.007   0.002   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 ( 6331)
  covalent geometry    : angle       0.71156 ( 8542)
  hydrogen bonds       : bond        0.04926 (  319)
  hydrogen bonds       : angle       5.23656 (  897)

*********************** 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
  112 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8231 (t)
REVERT: A   41 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7097 (t0)
REVERT: A   43 LYS cc_start: 0.8354 (mttt) cc_final: 0.7727 (pptt)
REVERT: A  143 ARG cc_start: 0.7203 (ttt180) cc_final: 0.6867 (ttt-90)
REVERT: A  257 LYS cc_start: 0.7893 (tttt) cc_final: 0.7405 (mmtp)
REVERT: A  263 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8715 (mm)
REVERT: A  330 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8049 (mtp)
REVERT: A  374 GLU cc_start: 0.8379 (tt0) cc_final: 0.7064 (tp30)
REVERT: A  482 ASN cc_start: 0.8346 (m-40) cc_final: 0.8029 (m110)
REVERT: A  511 ILE cc_start: 0.8251 (mm) cc_final: 0.7944 (mt)
REVERT: A  539 MET cc_start: 0.7271 (mmp) cc_final: 0.6436 (mmm)
REVERT: A  595 GLN cc_start: 0.7713 (mt0) cc_final: 0.7284 (mm110)
REVERT: A  720 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7157 (tt0)
REVERT: A  723 ARG cc_start: 0.8230 (ttt90) cc_final: 0.8017 (ttt-90)
REVERT: A  780 ARG cc_start: 0.6681 (mtt90) cc_final: 0.6385 (mmm160)
REVERT: A  787 ARG cc_start: 0.6851 (mtt-85) cc_final: 0.5878 (ttp-170)
  outliers start: 23
  outliers final: 6
  residues processed: 100
  average time/residue: 0.5842
  time to fit residues: 61.0593
Evaluate side-chains
  95 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
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  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 48 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 66 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  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN
A 292 ASN
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.157814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130367 restraints weight = 7152.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.84
r_work: 0.3401 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2490

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= 0.141
  Angle     :  0.595   7.994   8542  Z= 0.297
  Chirality :  0.044   0.141    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.557  93.886    849
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 10.26 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.30), residues: 758
  helix:  0.67 (0.26), residues: 386
  sheet: -0.81 (0.56), residues: 72
  loop : -0.73 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 403 
 TYR   0.022   0.001   TYR A 194 
 PHE   0.013   0.001   PHE A 577 
 TRP   0.007   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6331)
  covalent geometry    : angle       0.59485 ( 8542)
  hydrogen bonds       : bond        0.03972 (  319)
  hydrogen bonds       : angle       4.97069 (  897)

*********************** 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
  118 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8284 (t)
REVERT: A   43 LYS cc_start: 0.8374 (mttt) cc_final: 0.7717 (pptt)
REVERT: A  143 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6811 (ttt-90)
REVERT: A  194 TYR cc_start: 0.8435 (t80) cc_final: 0.8190 (t80)
REVERT: A  228 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7936 (mp0)
REVERT: A  257 LYS cc_start: 0.7877 (tttt) cc_final: 0.7415 (mmtp)
REVERT: A  263 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8628 (mm)
REVERT: A  374 GLU cc_start: 0.8330 (tt0) cc_final: 0.7030 (tp30)
REVERT: A  418 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.6284 (mp10)
REVERT: A  511 ILE cc_start: 0.8182 (mm) cc_final: 0.7959 (mt)
REVERT: A  539 MET cc_start: 0.7293 (mmp) cc_final: 0.6481 (mmm)
REVERT: A  595 GLN cc_start: 0.7689 (mt0) cc_final: 0.7272 (mm110)
REVERT: A  720 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7198 (tt0)
REVERT: A  731 PRO cc_start: 0.8011 (Cg_endo) cc_final: 0.7553 (Cg_exo)
REVERT: A  787 ARG cc_start: 0.6895 (mtt-85) cc_final: 0.5898 (ttp-170)
  outliers start: 28
  outliers final: 10
  residues processed: 103
  average time/residue: 0.6512
  time to fit residues: 69.9045
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  : 0.147 
-------------------------------------------------------------------------------
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  526 LYS
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 34 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 56 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.6982

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.158327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131532 restraints weight = 7202.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.78
r_work: 0.3387 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6331  Z= 0.148
  Angle     :  0.595   7.924   8542  Z= 0.296
  Chirality :  0.043   0.145    923
  Planarity :  0.003   0.037   1099
  Dihedral  :  6.412  92.953    849
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 11.31 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.30), residues: 758
  helix:  0.79 (0.26), residues: 387
  sheet: -0.89 (0.56), residues: 72
  loop : -0.74 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 780 
 TYR   0.015   0.001   TYR A 194 
 PHE   0.017   0.001   PHE A 359 
 TRP   0.008   0.001   TRP A 112 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6331)
  covalent geometry    : angle       0.59509 ( 8542)
  hydrogen bonds       : bond        0.03902 (  319)
  hydrogen bonds       : angle       4.87078 (  897)

*********************** 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
  109 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8290 (t)
REVERT: A   43 LYS cc_start: 0.8398 (mttt) cc_final: 0.7692 (pttt)
REVERT: A  143 ARG cc_start: 0.7161 (ttt180) cc_final: 0.6861 (ttt-90)
REVERT: A  194 TYR cc_start: 0.8477 (t80) cc_final: 0.8256 (t80)
REVERT: A  228 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7959 (mp0)
REVERT: A  257 LYS cc_start: 0.7794 (tttt) cc_final: 0.7377 (mmtp)
REVERT: A  263 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8627 (mm)
REVERT: A  328 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7245 (mt-10)
REVERT: A  363 LYS cc_start: 0.7158 (mmtm) cc_final: 0.6911 (mtpt)
REVERT: A  374 GLU cc_start: 0.8322 (tt0) cc_final: 0.7049 (tp30)
REVERT: A  413 LYS cc_start: 0.7836 (ptpt) cc_final: 0.7165 (ptpp)
REVERT: A  418 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6319 (mp10)
REVERT: A  439 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8091 (ttm)
REVERT: A  511 ILE cc_start: 0.8223 (mm) cc_final: 0.8007 (mt)
REVERT: A  539 MET cc_start: 0.7362 (mmp) cc_final: 0.6572 (mmm)
REVERT: A  554 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7258 (m-30)
REVERT: A  595 GLN cc_start: 0.7712 (mt0) cc_final: 0.7271 (mm110)
REVERT: A  720 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7251 (tt0)
REVERT: A  731 PRO cc_start: 0.7961 (Cg_endo) cc_final: 0.7575 (Cg_exo)
REVERT: A  787 ARG cc_start: 0.6881 (mtt-85) cc_final: 0.5857 (ttp-170)
  outliers start: 26
  outliers final: 7
  residues processed: 100
  average time/residue: 0.6330
  time to fit residues: 65.9964
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  : 0.453 
-------------------------------------------------------------------------------
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  439 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   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  44 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.156727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.129257 restraints weight = 7077.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.83
r_work: 0.3379 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6331  Z= 0.158
  Angle     :  0.594   8.232   8542  Z= 0.295
  Chirality :  0.044   0.143    923
  Planarity :  0.003   0.037   1099
  Dihedral  :  6.352  93.284    849
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 11.76 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.30), residues: 758
  helix:  0.79 (0.26), residues: 390
  sheet: -0.97 (0.56), residues: 72
  loop : -0.80 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 403 
 TYR   0.013   0.001   TYR A 266 
 PHE   0.016   0.001   PHE A 359 
 TRP   0.007   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6331)
  covalent geometry    : angle       0.59382 ( 8542)
  hydrogen bonds       : bond        0.03923 (  319)
  hydrogen bonds       : angle       4.83014 (  897)

*********************** 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
  112 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 83
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8306 (t)
REVERT: A   43 LYS cc_start: 0.8397 (mttt) cc_final: 0.7715 (ttpt)
REVERT: A  143 ARG cc_start: 0.7159 (ttt180) cc_final: 0.6873 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7962 (mp0)
REVERT: A  257 LYS cc_start: 0.7828 (tttt) cc_final: 0.7329 (mmtp)
REVERT: A  263 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8637 (mm)
REVERT: A  328 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7211 (mt-10)
REVERT: A  363 LYS cc_start: 0.7146 (mmtm) cc_final: 0.6902 (mtpt)
REVERT: A  418 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6329 (mp10)
REVERT: A  455 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7699 (m-80)
REVERT: A  511 ILE cc_start: 0.8221 (mm) cc_final: 0.8013 (mt)
REVERT: A  539 MET cc_start: 0.7351 (mmp) cc_final: 0.6562 (mmm)
REVERT: A  554 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7279 (m-30)
REVERT: A  595 GLN cc_start: 0.7734 (mt0) cc_final: 0.7267 (mm110)
REVERT: A  720 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7265 (tt0)
REVERT: A  787 ARG cc_start: 0.6890 (mtt-85) cc_final: 0.5888 (ttp-170)
  outliers start: 29
  outliers final: 10
  residues processed: 103
  average time/residue: 0.6198
  time to fit residues: 66.5161
Evaluate side-chains
  95 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
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  186 VAL
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  455 TYR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0870
   chunk 70 optimal weight:    0.0770
   chunk 20 optimal weight:    0.3980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.4918

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.158313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.130897 restraints weight = 7171.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.83
r_work: 0.3403 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2931

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     :  0.564   8.968   8542  Z= 0.280
  Chirality :  0.042   0.140    923
  Planarity :  0.003   0.035   1099
  Dihedral  :  6.147  90.615    849
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 13.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.30), residues: 758
  helix:  0.99 (0.26), residues: 388
  sheet: -1.03 (0.55), residues: 72
  loop : -0.62 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 403 
 TYR   0.012   0.001   TYR A 266 
 PHE   0.014   0.001   PHE A 577 
 TRP   0.006   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6331)
  covalent geometry    : angle       0.56361 ( 8542)
  hydrogen bonds       : bond        0.03569 (  319)
  hydrogen bonds       : angle       4.76537 (  897)

*********************** 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
  108 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8331 (t)
REVERT: A   43 LYS cc_start: 0.8415 (mttt) cc_final: 0.7717 (ttpt)
REVERT: A  143 ARG cc_start: 0.7157 (ttt180) cc_final: 0.6849 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7930 (mp0)
REVERT: A  257 LYS cc_start: 0.7845 (tttt) cc_final: 0.7365 (mmtp)
REVERT: A  263 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8619 (mm)
REVERT: A  328 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7159 (mt-10)
REVERT: A  363 LYS cc_start: 0.7159 (mmtm) cc_final: 0.6942 (mtpt)
REVERT: A  374 GLU cc_start: 0.8166 (tt0) cc_final: 0.7748 (mt-10)
REVERT: A  418 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.6357 (mp10)
REVERT: A  455 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7587 (m-80)
REVERT: A  539 MET cc_start: 0.7311 (mmp) cc_final: 0.6541 (mmm)
REVERT: A  554 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7280 (m-30)
REVERT: A  595 GLN cc_start: 0.7700 (mt0) cc_final: 0.7269 (mm110)
REVERT: A  645 GLN cc_start: 0.6551 (tp40) cc_final: 0.5574 (pt0)
REVERT: A  720 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7295 (tt0)
REVERT: A  740 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7744 (pttm)
REVERT: A  787 ARG cc_start: 0.6854 (mtt-85) cc_final: 0.5912 (ttp-170)
  outliers start: 21
  outliers final: 10
  residues processed: 100
  average time/residue: 0.6199
  time to fit residues: 64.5775
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  : 0.222 
-------------------------------------------------------------------------------
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  263 ILE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  455 TYR
Chi-restraints excluded: chain A residue  521 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  740 LYS
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 10 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.157883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.131151 restraints weight = 7165.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.77
r_work: 0.3410 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3006

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= 0.161
  Angle     :  0.601  10.549   8542  Z= 0.296
  Chirality :  0.044   0.143    923
  Planarity :  0.004   0.037   1099
  Dihedral  :  6.236  92.652    849
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 13.42 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.30), residues: 758
  helix:  0.91 (0.26), residues: 390
  sheet: -1.10 (0.55), residues: 72
  loop : -0.70 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 403 
 TYR   0.014   0.001   TYR A 266 
 PHE   0.015   0.001   PHE A 359 
 TRP   0.006   0.001   TRP A 112 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6331)
  covalent geometry    : angle       0.60127 ( 8542)
  hydrogen bonds       : bond        0.03876 (  319)
  hydrogen bonds       : angle       4.80882 (  897)

*********************** 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
  102 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8216 (t)
REVERT: A   43 LYS cc_start: 0.8421 (mttt) cc_final: 0.7719 (ttpt)
REVERT: A  143 ARG cc_start: 0.7187 (ttt180) cc_final: 0.6887 (ttt-90)
REVERT: A  228 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7955 (mp0)
REVERT: A  257 LYS cc_start: 0.7924 (tttt) cc_final: 0.7498 (mmtp)
REVERT: A  263 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8641 (mm)
REVERT: A  328 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7285 (mt-10)
REVERT: A  418 GLN cc_start: 0.6717 (OUTLIER) cc_final: 0.6447 (mp10)
REVERT: A  455 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7681 (m-80)
REVERT: A  482 ASN cc_start: 0.8296 (m-40) cc_final: 0.8014 (m110)
REVERT: A  526 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7166 (mptt)
REVERT: A  539 MET cc_start: 0.7340 (mmp) cc_final: 0.6581 (mmm)
REVERT: A  554 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7286 (m-30)
REVERT: A  595 GLN cc_start: 0.7791 (mt0) cc_final: 0.7376 (mm110)
REVERT: A  645 GLN cc_start: 0.6595 (tp40) cc_final: 0.5633 (pt0)
REVERT: A  720 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7364 (tt0)
REVERT: A  787 ARG cc_start: 0.6919 (mtt-85) cc_final: 0.6007 (ttp-170)
  outliers start: 21
  outliers final: 9
  residues processed: 96
  average time/residue: 0.5945
  time to fit residues: 59.7087
Evaluate side-chains
  97 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  186 VAL
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  455 TYR
Chi-restraints excluded: chain A residue  526 LYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   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 = 0.3855 r_free = 0.3855 target = 0.159248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.132361 restraints weight = 7190.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.80
r_work: 0.3398 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6331  Z= 0.139
  Angle     :  0.580  10.951   8542  Z= 0.284
  Chirality :  0.042   0.141    923
  Planarity :  0.003   0.035   1099
  Dihedral  :  6.149  91.321    849
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 13.42 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.30), residues: 758
  helix:  1.02 (0.26), residues: 389
  sheet: -1.11 (0.55), residues: 72
  loop : -0.60 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 403 
 TYR   0.025   0.001   TYR A 194 
 PHE   0.014   0.001   PHE A 577 
 TRP   0.007   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6331)
  covalent geometry    : angle       0.57969 ( 8542)
  hydrogen bonds       : bond        0.03661 (  319)
  hydrogen bonds       : angle       4.75265 (  897)

*********************** 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
  105 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8284 (t)
REVERT: A   43 LYS cc_start: 0.8396 (mttt) cc_final: 0.7675 (ttpt)
REVERT: A  143 ARG cc_start: 0.7173 (ttt180) cc_final: 0.6872 (ttt-90)
REVERT: A  194 TYR cc_start: 0.8408 (t80) cc_final: 0.8176 (t80)
REVERT: A  228 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7963 (mp0)
REVERT: A  257 LYS cc_start: 0.7908 (tttt) cc_final: 0.7452 (mmtp)
REVERT: A  263 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8641 (mm)
REVERT: A  328 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7268 (mt-10)
REVERT: A  374 GLU cc_start: 0.8175 (tt0) cc_final: 0.7734 (mt-10)
REVERT: A  418 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.6356 (mp10)
REVERT: A  455 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7682 (m-80)
REVERT: A  526 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7093 (mptt)
REVERT: A  539 MET cc_start: 0.7331 (mmp) cc_final: 0.6557 (mmm)
REVERT: A  554 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7293 (m-30)
REVERT: A  595 GLN cc_start: 0.7753 (mt0) cc_final: 0.7306 (mm110)
REVERT: A  645 GLN cc_start: 0.6677 (tp40) cc_final: 0.5715 (pt0)
REVERT: A  720 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7340 (tt0)
REVERT: A  787 ARG cc_start: 0.6834 (mtt-85) cc_final: 0.5924 (ttp-170)
  outliers start: 23
  outliers final: 10
  residues processed: 98
  average time/residue: 0.5639
  time to fit residues: 57.8721
Evaluate side-chains
  94 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
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  263 ILE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  455 TYR
Chi-restraints excluded: chain A residue  521 ILE
Chi-restraints excluded: chain A residue  526 LYS
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 22 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 63 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  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 = 0.3862 r_free = 0.3862 target = 0.159574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.132826 restraints weight = 7102.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.78
r_work: 0.3433 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6331  Z= 0.136
  Angle     :  0.588  11.987   8542  Z= 0.288
  Chirality :  0.042   0.142    923
  Planarity :  0.003   0.036   1099
  Dihedral  :  6.099  89.702    849
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.30), residues: 758
  helix:  1.03 (0.26), residues: 390
  sheet: -1.06 (0.55), residues: 72
  loop : -0.62 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 403 
 TYR   0.021   0.001   TYR A 194 
 PHE   0.014   0.001   PHE A 577 
 TRP   0.007   0.001   TRP A 130 
 HIS   0.002   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6331)
  covalent geometry    : angle       0.58786 ( 8542)
  hydrogen bonds       : bond        0.03625 (  319)
  hydrogen bonds       : angle       4.74946 (  897)

********************** 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
  99 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   28 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8248 (t)
REVERT: A   43 LYS cc_start: 0.8347 (mttt) cc_final: 0.7701 (ttpt)
REVERT: A  143 ARG cc_start: 0.7167 (ttt180) cc_final: 0.6880 (ttt-90)
REVERT: A  194 TYR cc_start: 0.8400 (t80) cc_final: 0.8176 (t80)
REVERT: A  228 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7969 (mp0)
REVERT: A  257 LYS cc_start: 0.7771 (tttt) cc_final: 0.7346 (mmtp)
REVERT: A  263 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8610 (mm)
REVERT: A  328 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7269 (mt-10)
REVERT: A  374 GLU cc_start: 0.8202 (tt0) cc_final: 0.7883 (mt-10)
REVERT: A  418 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6415 (mp10)
REVERT: A  455 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7670 (m-80)
REVERT: A  482 ASN cc_start: 0.8243 (m-40) cc_final: 0.7957 (m110)
REVERT: A  539 MET cc_start: 0.7277 (mmp) cc_final: 0.6525 (mmm)
REVERT: A  554 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7304 (m-30)
REVERT: A  595 GLN cc_start: 0.7758 (mt0) cc_final: 0.7353 (mm110)
REVERT: A  645 GLN cc_start: 0.6551 (tp40) cc_final: 0.5597 (pt0)
REVERT: A  720 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7367 (tt0)
REVERT: A  787 ARG cc_start: 0.6856 (mtt-85) cc_final: 0.5974 (ttp-170)
  outliers start: 18
  outliers final: 9
  residues processed: 93
  average time/residue: 0.5992
  time to fit residues: 58.1609
Evaluate side-chains
  94 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
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  263 ILE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  455 TYR
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 9 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.157869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.131137 restraints weight = 7103.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 1.77
r_work: 0.3410 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6331  Z= 0.166
  Angle     :  0.620  12.086   8542  Z= 0.303
  Chirality :  0.044   0.143    923
  Planarity :  0.004   0.036   1099
  Dihedral  :  6.216  91.589    849
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.03 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.30), residues: 758
  helix:  0.97 (0.26), residues: 390
  sheet: -1.08 (0.55), residues: 72
  loop : -0.64 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 403 
 TYR   0.023   0.002   TYR A 194 
 PHE   0.014   0.001   PHE A 577 
 TRP   0.006   0.001   TRP A 112 
 HIS   0.004   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6331)
  covalent geometry    : angle       0.62013 ( 8542)
  hydrogen bonds       : bond        0.03828 (  319)
  hydrogen bonds       : angle       4.77671 (  897)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2299.86 seconds
wall clock time: 40 minutes 2.60 seconds (2402.60 seconds total)