Starting phenix.real_space_refine
on Tue Mar  3 15:53:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xe6_22144/03_2026/6xe6_22144.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xe6_22144/03_2026/6xe6_22144.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xe6_22144/03_2026/6xe6_22144.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xe6_22144/03_2026/6xe6_22144.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xe6_22144/03_2026/6xe6_22144.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xe6_22144/03_2026/6xe6_22144.cif"
  }
  resolution = 4.53
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    4298      2.51       5
     N    1022      2.21       5
     O    1156      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6530
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 826, 6340
          Classifications: {'peptide': 826}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 36, 'TRANS': 789}
          Chain breaks: 10
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 259
          Unresolved non-hydrogen angles: 335
          Unresolved non-hydrogen dihedrals: 232
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 3, 'PHE:plan': 4, 'TRP:plan': 3, 'ASP:plan': 5, 'HIS:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 150
    Chain: "A"
      Number of atoms: 190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 190
          Unusual residues: {'NAG': 1, 'Y01': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 1.41, per 1000 atoms: 0.22
  Number of scatterers: 6530
  At special positions: 0
  Unit cell: (99.96, 74.97, 119.119, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1156      8.00
     N    1022      7.00
     C    4298      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 323 " - pdb=" SG  CYS A 367 " distance=2.04

  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: 0.50
  Conformation dependent library (CDL) restraints added in 254.4 milliseconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      62.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 188
      removed outlier: 3.547A  pdb=" N   TRP A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 210
    Processing helix  chain 'A' and resid 229 through 243
    Processing helix  chain 'A' and resid 320 through 327
      removed outlier: 3.534A  pdb=" N   ASN A 324 " --> pdb=" O   LYS A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 359
    Processing helix  chain 'A' and resid 370 through 385
      removed outlier: 4.701A  pdb=" N   CYS A 385 " --> pdb=" O   LEU A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 432
      removed outlier: 3.974A  pdb=" N   ILE A 427 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LEU A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 472
    Processing helix  chain 'A' and resid 491 through 523
      removed outlier: 4.545A  pdb=" N   GLN A 497 " --> pdb=" O   HIS A 493 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   LEU A 501 " --> pdb=" O   GLN A 497 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   MET A 502 " --> pdb=" O   ASP A 498 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TYR A 506 " --> pdb=" O   MET A 502 " (cutoff:3.500A)
      Proline residue:  A 507  - end of helix
      removed outlier: 3.527A  pdb=" N   LYS A 523 " --> pdb=" O   CYS A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 549
      removed outlier: 3.562A  pdb=" N   THR A 528 " --> pdb=" O   SER A 524 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 549 " --> pdb=" O   LEU A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 570
      removed outlier: 3.792A  pdb=" N   THR A 561 " --> pdb=" O   PHE A 557 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   LEU A 563 " --> pdb=" O   ASN A 559 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ILE A 564 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 569 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 588
      removed outlier: 3.713A  pdb=" N   PHE A 575 " --> pdb=" O   ALA A 571 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL A 576 " --> pdb=" O   ASP A 572 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ASP A 579 " --> pdb=" O   PHE A 575 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   VAL A 580 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE A 586 " --> pdb=" O   ASN A 582 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP A 587 " --> pdb=" O   TYR A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 623
      removed outlier: 3.617A  pdb=" N   THR A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA A 618 " --> pdb=" O   THR A 614 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   PHE A 619 " --> pdb=" O   THR A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 661
      removed outlier: 3.827A  pdb=" N   ARG A 631 " --> pdb=" O   ILE A 627 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A 645 " --> pdb=" O   ILE A 641 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL A 646 " --> pdb=" O   LEU A 642 " (cutoff:3.500A)
      Proline residue:  A 653  - end of helix
    Processing helix  chain 'A' and resid 689 through 716
      Proline residue:  A 711  - end of helix
    Processing helix  chain 'A' and resid 719 through 736
      removed outlier: 3.874A  pdb=" N   PHE A 723 " --> pdb=" O   TYR A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 769
      removed outlier: 3.659A  pdb=" N   ARG A 763 " --> pdb=" O   HIS A 759 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ASP A 765 " --> pdb=" O   PHE A 761 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ALA A 766 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 837
    Processing helix  chain 'A' and resid 852 through 862
      removed outlier: 3.613A  pdb=" N   PHE A 856 " --> pdb=" O   PHE A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 896
    Processing helix  chain 'A' and resid 938 through 955
      removed outlier: 3.558A  pdb=" N   GLN A 942 " --> pdb=" O   GLU A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 1003
      removed outlier: 3.507A  pdb=" N   ASP A 975 " --> pdb=" O   LEU A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1030
      removed outlier: 3.569A  pdb=" N   GLY A1025 " --> pdb=" O   PHE A1021 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   VAL A1028 " --> pdb=" O   VAL A1024 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU A1030 " --> pdb=" O   SER A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1062
      removed outlier: 3.987A  pdb=" N   HIS A1055 " --> pdb=" O   ASP A1051 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A1059 " --> pdb=" O   HIS A1055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1096
      removed outlier: 4.625A  pdb=" N   MET A1085 " --> pdb=" O   SER A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1134
      removed outlier: 3.690A  pdb=" N   THR A1106 " --> pdb=" O   VAL A1102 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ALA A1121 " --> pdb=" O   CYS A1117 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   CYS A1133 " --> pdb=" O   CYS A1129 " (cutoff:3.500A)

    357 hydrogen bonds defined for protein.
    1071 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: 0.83

  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:
        1.20 -     1.33: 1050
        1.33 -     1.45: 1802
        1.45 -     1.57: 3758
        1.57 -     1.70: 3
        1.70 -     1.82: 85
  Bond restraints: 6698
  Sorted by residual:
  bond pdb=" CAX Y01 A1303 "
       pdb=" OAH Y01 A1303 "
    ideal  model  delta    sigma   weight residual
    1.248  1.345 -0.097 2.00e-02 2.50e+03 2.33e+01
  bond pdb=" CAX Y01 A1304 "
       pdb=" OAH Y01 A1304 "
    ideal  model  delta    sigma   weight residual
    1.248  1.344 -0.096 2.00e-02 2.50e+03 2.32e+01
  bond pdb=" CAX Y01 A1302 "
       pdb=" OAH Y01 A1302 "
    ideal  model  delta    sigma   weight residual
    1.248  1.344 -0.096 2.00e-02 2.50e+03 2.32e+01
  bond pdb=" CAX Y01 A1305 "
       pdb=" OAH Y01 A1305 "
    ideal  model  delta    sigma   weight residual
    1.248  1.344 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" CAX Y01 A1301 "
       pdb=" OAH Y01 A1301 "
    ideal  model  delta    sigma   weight residual
    1.248  1.343 -0.095 2.00e-02 2.50e+03 2.25e+01
  ... (remaining 6693 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 8057
        2.13 -     4.26: 989
        4.26 -     6.39: 74
        6.39 -     8.52: 14
        8.52 -    10.65: 4
  Bond angle restraints: 9138
  Sorted by residual:
  angle pdb=" C   HIS A 759 "
        pdb=" N   PRO A 760 "
        pdb=" CA  PRO A 760 "
      ideal   model   delta    sigma   weight residual
     119.84  130.49  -10.65 1.25e+00 6.40e-01 7.26e+01
  angle pdb=" N   PRO A 439 "
        pdb=" CA  PRO A 439 "
        pdb=" CB  PRO A 439 "
      ideal   model   delta    sigma   weight residual
     103.25  111.16   -7.91 1.05e+00 9.07e-01 5.67e+01
  angle pdb=" N   PRO A 447 "
        pdb=" CA  PRO A 447 "
        pdb=" CB  PRO A 447 "
      ideal   model   delta    sigma   weight residual
     103.00  110.09   -7.09 1.10e+00 8.26e-01 4.16e+01
  angle pdb=" N   PRO A 415 "
        pdb=" CA  PRO A 415 "
        pdb=" CB  PRO A 415 "
      ideal   model   delta    sigma   weight residual
     103.00  109.71   -6.71 1.10e+00 8.26e-01 3.72e+01
  angle pdb=" N   TYR A 300 "
        pdb=" CA  TYR A 300 "
        pdb=" C   TYR A 300 "
      ideal   model   delta    sigma   weight residual
     111.03  117.61   -6.58 1.11e+00 8.12e-01 3.52e+01
  ... (remaining 9133 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 3725
       17.13 -    34.26: 331
       34.26 -    51.40: 102
       51.40 -    68.53: 16
       68.53 -    85.66: 2
  Dihedral angle restraints: 4176
    sinusoidal: 1753
      harmonic: 2423
  Sorted by residual:
  dihedral pdb=" CA  LYS A 588 "
           pdb=" C   LYS A 588 "
           pdb=" N   PRO A 589 "
           pdb=" CA  PRO A 589 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.51  -29.49     0      5.00e+00 4.00e-02 3.48e+01
  dihedral pdb=" CB  CYS A 323 "
           pdb=" SG  CYS A 323 "
           pdb=" SG  CYS A 367 "
           pdb=" CB  CYS A 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.42   47.58     1      1.00e+01 1.00e-02 3.12e+01
  dihedral pdb=" CA  ALA A1082 "
           pdb=" C   ALA A1082 "
           pdb=" N   MET A1083 "
           pdb=" CA  MET A1083 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.97  -26.03     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 4173 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 852
       0.078 -    0.157: 179
       0.157 -    0.235: 33
       0.235 -    0.313: 7
       0.313 -    0.392: 5
  Chirality restraints: 1076
  Sorted by residual:
  chirality pdb=" CBG Y01 A1303 "
            pdb=" CAQ Y01 A1303 "
            pdb=" CBD Y01 A1303 "
            pdb=" CBI Y01 A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.72    0.39 2.00e-01 2.50e+01 3.84e+00
  chirality pdb=" CBG Y01 A1305 "
            pdb=" CAQ Y01 A1305 "
            pdb=" CBD Y01 A1305 "
            pdb=" CBI Y01 A1305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.38 2.00e-01 2.50e+01 3.54e+00
  chirality pdb=" CBG Y01 A1304 "
            pdb=" CAQ Y01 A1304 "
            pdb=" CBD Y01 A1304 "
            pdb=" CBI Y01 A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.37 2.00e-01 2.50e+01 3.49e+00
  ... (remaining 1073 not shown)

  Planarity restraints: 1104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 879 "   -0.043 5.00e-02 4.00e+02   6.51e-02 6.78e+00
        pdb=" N   PRO A 880 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 880 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 880 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 876 "    0.022 2.00e-02 2.50e+03   1.94e-02 5.64e+00
        pdb=" CG  HIS A 876 "   -0.037 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 876 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 876 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 876 "    0.017 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 876 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 316 "    0.039 5.00e-02 4.00e+02   5.88e-02 5.53e+00
        pdb=" N   PRO A 317 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1101 not shown)

  Histogram of nonbonded interaction distances:
        1.10 -     1.86: 3
        1.86 -     2.62: 42
        2.62 -     3.38: 9038
        3.38 -     4.14: 14438
        4.14 -     4.90: 24894
  Nonbonded interactions: 48415
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 836 "
            pdb=" O1  NAG A1306 "
     model   vdw
     1.098 3.040
  nonbonded pdb=" O   SER A 820 "
            pdb=" NE2 GLN A 883 "
     model   vdw
     1.733 3.120
  nonbonded pdb=" O   PRO A 910 "
            pdb=" O   ALA A 922 "
     model   vdw
     1.773 3.040
  nonbonded pdb=" CG  ASN A 836 "
            pdb=" O1  NAG A1306 "
     model   vdw
     2.181 3.270
  nonbonded pdb=" O   VAL A 610 "
            pdb=" OG1 THR A 614 "
     model   vdw
     2.266 3.040
  ... (remaining 48410 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.890
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
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      :  0.011   0.139   6699  Z= 0.739
  Angle     :  1.399  10.649   9140  Z= 0.913
  Chirality :  0.072   0.392   1076
  Planarity :  0.005   0.065   1104
  Dihedral  : 14.626  85.659   2597
  Min Nonbonded Distance : 1.098

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  1.24 %
    Allowed  : 11.32 %
    Favored  : 87.44 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.38 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.25 %
  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 are not related in a simple way.
  whole: -4.98 (0.22), residues: 804
  helix: -2.36 (0.18), residues: 473
  sheet:  None (None), residues: 0
  loop : -4.80 (0.25), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1078 
 TYR   0.019   0.002   TYR A 764 
 PHE   0.024   0.003   PHE A 839 
 TRP   0.019   0.002   TRP A 826 
 HIS   0.017   0.002   HIS A 876 

Details of bonding type rmsd
  covalent geometry    : bond        0.01083 ( 6698)
  covalent geometry    : angle       1.39858 ( 9138)
  SS BOND              : bond        0.00764 (    1)
  SS BOND              : angle       1.43864 (    2)
  hydrogen bonds       : bond        0.19759 (  357)
  hydrogen bonds       : angle       8.13855 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 232
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  220 LEU cc_start: 0.9011 (pp) cc_final: 0.8792 (pp)
REVERT: A  221 LEU cc_start: 0.9445 (tp) cc_final: 0.9056 (tp)
REVERT: A  383 ARG cc_start: 0.7858 (mtt180) cc_final: 0.6452 (tpt-90)
REVERT: A  433 ASP cc_start: 0.7710 (m-30) cc_final: 0.7435 (m-30)
REVERT: A  453 MET cc_start: 0.5448 (pmm) cc_final: 0.4694 (pmm)
REVERT: A  465 MET cc_start: 0.8420 (ttt) cc_final: 0.7960 (tpt)
REVERT: A  573 ASP cc_start: 0.8357 (m-30) cc_final: 0.7791 (m-30)
REVERT: A  578 CYS cc_start: 0.8937 (m) cc_final: 0.8594 (m)
REVERT: A  581 TRP cc_start: 0.8950 (t-100) cc_final: 0.8185 (t-100)
REVERT: A  597 VAL cc_start: 0.9693 (p) cc_final: 0.9402 (p)
REVERT: A  620 TYR cc_start: 0.8790 (m-80) cc_final: 0.8145 (m-80)
REVERT: A  796 GLU cc_start: 0.8965 (tt0) cc_final: 0.8687 (tt0)
REVERT: A  798 ASN cc_start: 0.7981 (p0) cc_final: 0.7289 (t0)
REVERT: A  970 ASN cc_start: 0.8277 (p0) cc_final: 0.8018 (p0)
REVERT: A 1011 TYR cc_start: 0.8822 (m-10) cc_final: 0.6857 (m-80)
REVERT: A 1029 LEU cc_start: 0.9265 (tp) cc_final: 0.9003 (tp)
REVERT: A 1032 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.6775 (t60)
REVERT: A 1034 LEU cc_start: 0.9423 (tt) cc_final: 0.8887 (mp)
REVERT: A 1052 PHE cc_start: 0.8248 (m-80) cc_final: 0.8013 (m-80)
REVERT: A 1083 MET cc_start: 0.8866 (mmp) cc_final: 0.8646 (mmm)
REVERT: A 1101 THR cc_start: 0.9146 (m) cc_final: 0.8946 (m)
REVERT: A 1112 MET cc_start: 0.8317 (ppp) cc_final: 0.7542 (ppp)
  outliers start: 7
  outliers final: 2
  residues processed: 236
  average time/residue: 0.0641
  time to fit residues: 21.3736
Evaluate side-chains
  188 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 185
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 363 ASN
A 559 ASN
A 941 HIS
A1128 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.135906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.112988 restraints weight = 14038.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.116692 restraints weight = 8641.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.119228 restraints weight = 5877.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.121115 restraints weight = 4344.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.122227 restraints weight = 3378.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6699  Z= 0.182
  Angle     :  0.772   8.964   9140  Z= 0.400
  Chirality :  0.046   0.233   1076
  Planarity :  0.005   0.041   1104
  Dihedral  :  8.732  56.274   1248
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.07 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.61 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 are not related in a simple way.
  whole: -2.97 (0.27), residues: 804
  helix: -0.55 (0.22), residues: 485
  sheet:  None (None), residues: 0
  loop : -4.39 (0.28), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1132 
 TYR   0.034   0.002   TYR A1011 
 PHE   0.032   0.003   PHE A 725 
 TRP   0.026   0.002   TRP A 826 
 HIS   0.006   0.001   HIS A 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 6698)
  covalent geometry    : angle       0.77140 ( 9138)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       1.34308 (    2)
  hydrogen bonds       : bond        0.05829 (  357)
  hydrogen bonds       : angle       5.16926 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 211
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9301 (tp) cc_final: 0.8901 (tp)
REVERT: A  302 ARG cc_start: 0.7147 (ptt-90) cc_final: 0.6910 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7851 (mtt180) cc_final: 0.6556 (tpt-90)
REVERT: A  453 MET cc_start: 0.4773 (pmm) cc_final: 0.4562 (pmm)
REVERT: A  465 MET cc_start: 0.8340 (ttt) cc_final: 0.7930 (tpp)
REVERT: A  540 ILE cc_start: 0.9351 (pt) cc_final: 0.9140 (tp)
REVERT: A  573 ASP cc_start: 0.8747 (m-30) cc_final: 0.8368 (m-30)
REVERT: A  578 CYS cc_start: 0.9314 (m) cc_final: 0.9029 (m)
REVERT: A  581 TRP cc_start: 0.8937 (t-100) cc_final: 0.8011 (t-100)
REVERT: A  596 THR cc_start: 0.9391 (p) cc_final: 0.9119 (p)
REVERT: A  597 VAL cc_start: 0.9751 (p) cc_final: 0.9413 (p)
REVERT: A  636 TYR cc_start: 0.8724 (t80) cc_final: 0.8519 (t80)
REVERT: A  645 TYR cc_start: 0.9445 (t80) cc_final: 0.9239 (t80)
REVERT: A  725 PHE cc_start: 0.8456 (t80) cc_final: 0.8048 (t80)
REVERT: A  765 ASP cc_start: 0.7144 (m-30) cc_final: 0.6877 (m-30)
REVERT: A  796 GLU cc_start: 0.8917 (tt0) cc_final: 0.8028 (tm-30)
REVERT: A  798 ASN cc_start: 0.7946 (p0) cc_final: 0.7212 (t0)
REVERT: A  858 GLN cc_start: 0.9364 (mm-40) cc_final: 0.9159 (mm-40)
REVERT: A  927 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8886 (m-10)
REVERT: A  950 TRP cc_start: 0.8806 (t-100) cc_final: 0.8454 (t-100)
REVERT: A 1043 SER cc_start: 0.9359 (m) cc_final: 0.9035 (t)
REVERT: A 1083 MET cc_start: 0.8787 (mmp) cc_final: 0.8425 (mmp)
REVERT: A 1101 THR cc_start: 0.9059 (m) cc_final: 0.8835 (m)
REVERT: A 1112 MET cc_start: 0.8439 (ppp) cc_final: 0.8013 (ppp)
REVERT: A 1113 MET cc_start: 0.8701 (ttp) cc_final: 0.7726 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0535
  time to fit residues: 16.5962
Evaluate side-chains
  168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 837 GLN
** A 977 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 = 0.3736 r_free = 0.3736 target = 0.138862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.116268 restraints weight = 13783.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.120018 restraints weight = 8286.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.122690 restraints weight = 5552.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.124577 restraints weight = 4014.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.125959 restraints weight = 3103.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6699  Z= 0.151
  Angle     :  0.718  11.765   9140  Z= 0.365
  Chirality :  0.043   0.181   1076
  Planarity :  0.004   0.038   1104
  Dihedral  :  8.266  58.886   1248
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.45 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  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 are not related in a simple way.
  whole: -2.13 (0.29), residues: 804
  helix:  0.10 (0.23), residues: 481
  sheet:  None (None), residues: 0
  loop : -3.94 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 233 
 TYR   0.016   0.001   TYR A1011 
 PHE   0.022   0.002   PHE A 839 
 TRP   0.023   0.001   TRP A 826 
 HIS   0.007   0.001   HIS A 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6698)
  covalent geometry    : angle       0.71829 ( 9138)
  SS BOND              : bond        0.00257 (    1)
  SS BOND              : angle       1.21423 (    2)
  hydrogen bonds       : bond        0.05213 (  357)
  hydrogen bonds       : angle       4.78735 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 ASP cc_start: 0.8956 (t0) cc_final: 0.8739 (t0)
REVERT: A  220 LEU cc_start: 0.8757 (pp) cc_final: 0.8420 (pp)
REVERT: A  221 LEU cc_start: 0.9319 (tp) cc_final: 0.8842 (tp)
REVERT: A  233 ARG cc_start: 0.8879 (mtt180) cc_final: 0.8051 (mtt-85)
REVERT: A  383 ARG cc_start: 0.7888 (mtt180) cc_final: 0.6602 (tpt-90)
REVERT: A  453 MET cc_start: 0.4709 (pmm) cc_final: 0.3514 (pmm)
REVERT: A  465 MET cc_start: 0.8332 (ttt) cc_final: 0.7905 (tmm)
REVERT: A  536 ILE cc_start: 0.9137 (mm) cc_final: 0.8798 (mm)
REVERT: A  573 ASP cc_start: 0.8776 (m-30) cc_final: 0.8524 (m-30)
REVERT: A  578 CYS cc_start: 0.9313 (m) cc_final: 0.9062 (m)
REVERT: A  581 TRP cc_start: 0.8935 (t-100) cc_final: 0.7937 (t-100)
REVERT: A  596 THR cc_start: 0.9414 (p) cc_final: 0.9092 (p)
REVERT: A  597 VAL cc_start: 0.9742 (p) cc_final: 0.9469 (p)
REVERT: A  636 TYR cc_start: 0.8663 (t80) cc_final: 0.8426 (t80)
REVERT: A  645 TYR cc_start: 0.9359 (t80) cc_final: 0.9041 (t80)
REVERT: A  725 PHE cc_start: 0.8268 (t80) cc_final: 0.7783 (t80)
REVERT: A  765 ASP cc_start: 0.7134 (m-30) cc_final: 0.6723 (m-30)
REVERT: A  791 TRP cc_start: 0.8637 (m-10) cc_final: 0.8170 (m-10)
REVERT: A  796 GLU cc_start: 0.8911 (tt0) cc_final: 0.7925 (tm-30)
REVERT: A  798 ASN cc_start: 0.7824 (p0) cc_final: 0.7086 (t0)
REVERT: A 1083 MET cc_start: 0.8929 (mmp) cc_final: 0.8480 (mmp)
REVERT: A 1112 MET cc_start: 0.8487 (ppp) cc_final: 0.8082 (ppp)
REVERT: A 1113 MET cc_start: 0.8700 (ttp) cc_final: 0.7720 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0530
  time to fit residues: 16.0362
Evaluate side-chains
  169 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 644 ASN
** A 977 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 = 0.3731 r_free = 0.3731 target = 0.138465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.117980 restraints weight = 14336.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.121028 restraints weight = 9257.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.123154 restraints weight = 6516.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.124752 restraints weight = 4914.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.125926 restraints weight = 3914.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6699  Z= 0.151
  Angle     :  0.693   9.142   9140  Z= 0.358
  Chirality :  0.043   0.178   1076
  Planarity :  0.004   0.040   1104
  Dihedral  :  8.008  59.966   1248
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.45 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 are not related in a simple way.
  whole: -2.08 (0.29), residues: 804
  helix:  0.23 (0.23), residues: 487
  sheet: -5.26 (0.56), residues: 16
  loop : -4.02 (0.30), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 302 
 TYR   0.039   0.002   TYR A1011 
 PHE   0.022   0.002   PHE A 839 
 TRP   0.022   0.001   TRP A 826 
 HIS   0.005   0.001   HIS A 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6698)
  covalent geometry    : angle       0.69298 ( 9138)
  SS BOND              : bond        0.00268 (    1)
  SS BOND              : angle       1.05901 (    2)
  hydrogen bonds       : bond        0.05079 (  357)
  hydrogen bonds       : angle       4.69252 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8987 (pp) cc_final: 0.8636 (pp)
REVERT: A  221 LEU cc_start: 0.9406 (tp) cc_final: 0.8934 (tp)
REVERT: A  232 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7638 (mm-40)
REVERT: A  233 ARG cc_start: 0.8953 (mtt180) cc_final: 0.8688 (mtt-85)
REVERT: A  234 LEU cc_start: 0.9130 (tp) cc_final: 0.8860 (tp)
REVERT: A  302 ARG cc_start: 0.7307 (ptt-90) cc_final: 0.7051 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7759 (mtt180) cc_final: 0.6579 (tpt-90)
REVERT: A  453 MET cc_start: 0.5062 (pmm) cc_final: 0.3759 (pmm)
REVERT: A  465 MET cc_start: 0.8199 (ttt) cc_final: 0.7915 (tmm)
REVERT: A  536 ILE cc_start: 0.9071 (mm) cc_final: 0.8753 (mm)
REVERT: A  557 PHE cc_start: 0.9186 (p90) cc_final: 0.8950 (p90)
REVERT: A  578 CYS cc_start: 0.9238 (m) cc_final: 0.8790 (m)
REVERT: A  581 TRP cc_start: 0.8826 (t-100) cc_final: 0.7775 (t-100)
REVERT: A  596 THR cc_start: 0.9320 (p) cc_final: 0.9013 (p)
REVERT: A  597 VAL cc_start: 0.9641 (p) cc_final: 0.9337 (p)
REVERT: A  608 MET cc_start: 0.8896 (mtt) cc_final: 0.8481 (mtt)
REVERT: A  765 ASP cc_start: 0.6904 (m-30) cc_final: 0.6680 (m-30)
REVERT: A  796 GLU cc_start: 0.8616 (tt0) cc_final: 0.8063 (tm-30)
REVERT: A  798 ASN cc_start: 0.7615 (p0) cc_final: 0.6711 (t0)
REVERT: A  970 ASN cc_start: 0.8282 (p0) cc_final: 0.7989 (p0)
REVERT: A 1033 GLU cc_start: 0.9063 (pm20) cc_final: 0.8782 (pm20)
REVERT: A 1083 MET cc_start: 0.9110 (mmp) cc_final: 0.8189 (ttm)
REVERT: A 1112 MET cc_start: 0.8405 (ppp) cc_final: 0.7834 (ppp)
REVERT: A 1113 MET cc_start: 0.8484 (ttp) cc_final: 0.7569 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.0539
  time to fit residues: 16.1639
Evaluate side-chains
  168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 590 HIS
** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1055 HIS ** 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 = 0.3751 r_free = 0.3751 target = 0.140258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.118946 restraints weight = 14401.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.122248 restraints weight = 9107.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.124512 restraints weight = 6317.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.126216 restraints weight = 4732.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127335 restraints weight = 3730.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.4283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6699  Z= 0.150
  Angle     :  0.688   8.971   9140  Z= 0.354
  Chirality :  0.043   0.189   1076
  Planarity :  0.004   0.041   1104
  Dihedral  :  7.827  59.755   1248
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.45 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 are not related in a simple way.
  whole: -1.94 (0.29), residues: 804
  helix:  0.33 (0.23), residues: 488
  sheet: -4.99 (0.64), residues: 16
  loop : -3.97 (0.31), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1132 
 TYR   0.038   0.002   TYR A1011 
 PHE   0.018   0.002   PHE A 856 
 TRP   0.018   0.001   TRP A 826 
 HIS   0.005   0.001   HIS A 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6698)
  covalent geometry    : angle       0.68763 ( 9138)
  SS BOND              : bond        0.00242 (    1)
  SS BOND              : angle       1.01812 (    2)
  hydrogen bonds       : bond        0.04954 (  357)
  hydrogen bonds       : angle       4.67057 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9327 (tp) cc_final: 0.9042 (tp)
REVERT: A  302 ARG cc_start: 0.7477 (ptt-90) cc_final: 0.7252 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7772 (mtt180) cc_final: 0.6534 (tpt-90)
REVERT: A  453 MET cc_start: 0.5022 (pmm) cc_final: 0.3913 (pmm)
REVERT: A  465 MET cc_start: 0.8348 (ttt) cc_final: 0.7926 (tmm)
REVERT: A  536 ILE cc_start: 0.9056 (mm) cc_final: 0.8693 (mm)
REVERT: A  551 HIS cc_start: 0.9043 (m90) cc_final: 0.8819 (m90)
REVERT: A  578 CYS cc_start: 0.9293 (m) cc_final: 0.8944 (m)
REVERT: A  581 TRP cc_start: 0.8913 (t-100) cc_final: 0.7846 (t-100)
REVERT: A  584 THR cc_start: 0.9508 (p) cc_final: 0.9164 (p)
REVERT: A  587 ASP cc_start: 0.8774 (p0) cc_final: 0.7905 (m-30)
REVERT: A  596 THR cc_start: 0.9383 (p) cc_final: 0.9035 (p)
REVERT: A  597 VAL cc_start: 0.9690 (p) cc_final: 0.9409 (p)
REVERT: A  725 PHE cc_start: 0.8181 (t80) cc_final: 0.7841 (t80)
REVERT: A  765 ASP cc_start: 0.6876 (m-30) cc_final: 0.6532 (m-30)
REVERT: A  781 GLU cc_start: 0.8286 (tt0) cc_final: 0.7723 (tp30)
REVERT: A  791 TRP cc_start: 0.7692 (m-10) cc_final: 0.7312 (m-10)
REVERT: A  796 GLU cc_start: 0.8789 (tt0) cc_final: 0.8062 (tm-30)
REVERT: A  798 ASN cc_start: 0.7696 (p0) cc_final: 0.6854 (t0)
REVERT: A  970 ASN cc_start: 0.8237 (p0) cc_final: 0.8011 (p0)
REVERT: A  974 TYR cc_start: 0.8449 (t80) cc_final: 0.8225 (t80)
REVERT: A  977 GLN cc_start: 0.8692 (mm-40) cc_final: 0.7952 (mm-40)
REVERT: A 1007 ILE cc_start: 0.8616 (tt) cc_final: 0.8028 (tp)
REVERT: A 1033 GLU cc_start: 0.9097 (pm20) cc_final: 0.8773 (pm20)
REVERT: A 1083 MET cc_start: 0.8893 (mmp) cc_final: 0.8188 (ttm)
REVERT: A 1112 MET cc_start: 0.8439 (ppp) cc_final: 0.7881 (ppp)
REVERT: A 1113 MET cc_start: 0.8598 (ttp) cc_final: 0.7728 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0530
  time to fit residues: 16.0446
Evaluate side-chains
  165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0770
   chunk 72 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    1.1342

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 778 HIS
A 837 GLN
A 858 GLN
** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.140683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.119474 restraints weight = 13919.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.122749 restraints weight = 8852.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.125109 restraints weight = 6138.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.126740 restraints weight = 4548.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.127640 restraints weight = 3592.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6699  Z= 0.144
  Angle     :  0.698   7.950   9140  Z= 0.358
  Chirality :  0.043   0.198   1076
  Planarity :  0.004   0.044   1104
  Dihedral  :  7.752  59.971   1248
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.58 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 are not related in a simple way.
  whole: -1.77 (0.30), residues: 804
  helix:  0.37 (0.23), residues: 480
  sheet: -4.75 (0.72), residues: 16
  loop : -3.63 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 661 
 TYR   0.054   0.002   TYR A1011 
 PHE   0.018   0.002   PHE A 725 
 TRP   0.021   0.001   TRP A 826 
 HIS   0.011   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6698)
  covalent geometry    : angle       0.69808 ( 9138)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       1.04036 (    2)
  hydrogen bonds       : bond        0.04935 (  357)
  hydrogen bonds       : angle       4.64602 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8923 (pp) cc_final: 0.8602 (pp)
REVERT: A  221 LEU cc_start: 0.9393 (tp) cc_final: 0.8919 (tp)
REVERT: A  302 ARG cc_start: 0.7795 (ptt-90) cc_final: 0.7429 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7788 (mtt180) cc_final: 0.6555 (tpt-90)
REVERT: A  453 MET cc_start: 0.5164 (pmm) cc_final: 0.3932 (pmm)
REVERT: A  465 MET cc_start: 0.8278 (ttt) cc_final: 0.7990 (tmm)
REVERT: A  518 MET cc_start: 0.8713 (ttm) cc_final: 0.8104 (tpp)
REVERT: A  536 ILE cc_start: 0.9023 (mm) cc_final: 0.8667 (mm)
REVERT: A  573 ASP cc_start: 0.8085 (m-30) cc_final: 0.7599 (m-30)
REVERT: A  578 CYS cc_start: 0.9241 (m) cc_final: 0.8998 (m)
REVERT: A  581 TRP cc_start: 0.8877 (t-100) cc_final: 0.7842 (t-100)
REVERT: A  584 THR cc_start: 0.9498 (p) cc_final: 0.9166 (p)
REVERT: A  587 ASP cc_start: 0.8805 (p0) cc_final: 0.7885 (m-30)
REVERT: A  596 THR cc_start: 0.9395 (p) cc_final: 0.8991 (p)
REVERT: A  608 MET cc_start: 0.8858 (mtt) cc_final: 0.8320 (mtt)
REVERT: A  725 PHE cc_start: 0.8327 (t80) cc_final: 0.7791 (t80)
REVERT: A  765 ASP cc_start: 0.6810 (m-30) cc_final: 0.6495 (m-30)
REVERT: A  781 GLU cc_start: 0.8277 (tt0) cc_final: 0.7794 (tm-30)
REVERT: A  791 TRP cc_start: 0.7787 (m-10) cc_final: 0.7499 (m-10)
REVERT: A  796 GLU cc_start: 0.8761 (tt0) cc_final: 0.8035 (tm-30)
REVERT: A  798 ASN cc_start: 0.7647 (p0) cc_final: 0.6795 (t0)
REVERT: A 1112 MET cc_start: 0.8297 (ppp) cc_final: 0.7849 (ppp)
REVERT: A 1113 MET cc_start: 0.8606 (ttp) cc_final: 0.7690 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0518
  time to fit residues: 15.4170
Evaluate side-chains
  168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 858 GLN
** A 977 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 = 0.3750 r_free = 0.3750 target = 0.140398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.119778 restraints weight = 14329.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.122764 restraints weight = 9390.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.124852 restraints weight = 6697.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.126524 restraints weight = 5125.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.127478 restraints weight = 4088.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6699  Z= 0.160
  Angle     :  0.741   9.622   9140  Z= 0.377
  Chirality :  0.044   0.201   1076
  Planarity :  0.005   0.045   1104
  Dihedral  :  7.706  59.901   1248
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.07 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 are not related in a simple way.
  whole: -1.72 (0.29), residues: 804
  helix:  0.43 (0.23), residues: 481
  sheet: -4.61 (0.79), residues: 18
  loop : -3.65 (0.32), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1132 
 TYR   0.032   0.002   TYR A1011 
 PHE   0.022   0.002   PHE A 725 
 TRP   0.021   0.001   TRP A 826 
 HIS   0.010   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6698)
  covalent geometry    : angle       0.74131 ( 9138)
  SS BOND              : bond        0.00211 (    1)
  SS BOND              : angle       0.97090 (    2)
  hydrogen bonds       : bond        0.04948 (  357)
  hydrogen bonds       : angle       4.66618 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9390 (tp) cc_final: 0.9116 (tp)
REVERT: A  302 ARG cc_start: 0.7838 (ptt-90) cc_final: 0.7505 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7736 (mtt180) cc_final: 0.6533 (tpt-90)
REVERT: A  465 MET cc_start: 0.8589 (ttt) cc_final: 0.7480 (tmm)
REVERT: A  536 ILE cc_start: 0.9038 (mm) cc_final: 0.8690 (mm)
REVERT: A  558 MET cc_start: 0.9277 (mpp) cc_final: 0.8947 (mpp)
REVERT: A  578 CYS cc_start: 0.9193 (m) cc_final: 0.8857 (m)
REVERT: A  581 TRP cc_start: 0.8732 (t-100) cc_final: 0.7788 (t-100)
REVERT: A  596 THR cc_start: 0.9300 (p) cc_final: 0.9000 (p)
REVERT: A  725 PHE cc_start: 0.8421 (t80) cc_final: 0.7766 (t80)
REVERT: A  765 ASP cc_start: 0.6852 (m-30) cc_final: 0.6549 (m-30)
REVERT: A  781 GLU cc_start: 0.8271 (tt0) cc_final: 0.7831 (tm-30)
REVERT: A  791 TRP cc_start: 0.7803 (m-10) cc_final: 0.7380 (m-10)
REVERT: A  798 ASN cc_start: 0.7640 (p0) cc_final: 0.6749 (t0)
REVERT: A  811 THR cc_start: 0.8064 (p) cc_final: 0.7712 (p)
REVERT: A  970 ASN cc_start: 0.8273 (p0) cc_final: 0.8071 (p0)
REVERT: A 1007 ILE cc_start: 0.8237 (tt) cc_final: 0.7463 (tp)
REVERT: A 1083 MET cc_start: 0.9155 (mmp) cc_final: 0.8293 (mmm)
REVERT: A 1112 MET cc_start: 0.8232 (ppp) cc_final: 0.7781 (ppp)
REVERT: A 1113 MET cc_start: 0.8490 (ttp) cc_final: 0.7636 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.0528
  time to fit residues: 16.0876
Evaluate side-chains
  170 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 1 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 941 HIS
** A 977 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 = 0.3798 r_free = 0.3798 target = 0.143458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.122150 restraints weight = 14133.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.125395 restraints weight = 9005.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.127798 restraints weight = 6310.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.129428 restraints weight = 4712.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.130875 restraints weight = 3736.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.5117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6699  Z= 0.141
  Angle     :  0.737   9.038   9140  Z= 0.368
  Chirality :  0.044   0.197   1076
  Planarity :  0.004   0.047   1104
  Dihedral  :  7.565  57.985   1248
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.07 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 are not related in a simple way.
  whole: -1.57 (0.30), residues: 804
  helix:  0.57 (0.24), residues: 487
  sheet: -4.49 (0.83), residues: 18
  loop : -3.71 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1132 
 TYR   0.032   0.002   TYR A1011 
 PHE   0.015   0.001   PHE A 839 
 TRP   0.023   0.001   TRP A 651 
 HIS   0.011   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6698)
  covalent geometry    : angle       0.73674 ( 9138)
  SS BOND              : bond        0.00198 (    1)
  SS BOND              : angle       1.02412 (    2)
  hydrogen bonds       : bond        0.04786 (  357)
  hydrogen bonds       : angle       4.56386 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8900 (pp) cc_final: 0.8629 (pp)
REVERT: A  221 LEU cc_start: 0.9358 (tp) cc_final: 0.8828 (tp)
REVERT: A  228 THR cc_start: 0.9035 (p) cc_final: 0.8637 (p)
REVERT: A  383 ARG cc_start: 0.7740 (mtt180) cc_final: 0.6542 (tpp-160)
REVERT: A  465 MET cc_start: 0.8494 (ttt) cc_final: 0.7579 (tmm)
REVERT: A  518 MET cc_start: 0.8695 (ttm) cc_final: 0.8427 (ttm)
REVERT: A  536 ILE cc_start: 0.8968 (mm) cc_final: 0.8621 (mm)
REVERT: A  557 PHE cc_start: 0.9216 (p90) cc_final: 0.8983 (p90)
REVERT: A  578 CYS cc_start: 0.9211 (m) cc_final: 0.9008 (m)
REVERT: A  581 TRP cc_start: 0.8753 (t-100) cc_final: 0.7811 (t-100)
REVERT: A  584 THR cc_start: 0.9523 (p) cc_final: 0.9199 (p)
REVERT: A  587 ASP cc_start: 0.8841 (p0) cc_final: 0.7959 (m-30)
REVERT: A  596 THR cc_start: 0.9344 (p) cc_final: 0.9016 (p)
REVERT: A  608 MET cc_start: 0.9001 (mtt) cc_final: 0.8751 (mtt)
REVERT: A  725 PHE cc_start: 0.8312 (t80) cc_final: 0.7816 (t80)
REVERT: A  765 ASP cc_start: 0.6858 (m-30) cc_final: 0.6506 (m-30)
REVERT: A  781 GLU cc_start: 0.8281 (tt0) cc_final: 0.7785 (tm-30)
REVERT: A  791 TRP cc_start: 0.7906 (m-10) cc_final: 0.7411 (m-10)
REVERT: A  798 ASN cc_start: 0.8004 (p0) cc_final: 0.6768 (t0)
REVERT: A  810 LEU cc_start: 0.8894 (pt) cc_final: 0.8627 (pp)
REVERT: A  970 ASN cc_start: 0.8287 (p0) cc_final: 0.8080 (p0)
REVERT: A 1007 ILE cc_start: 0.8169 (tt) cc_final: 0.7355 (tp)
REVERT: A 1033 GLU cc_start: 0.9036 (pm20) cc_final: 0.8798 (pm20)
REVERT: A 1112 MET cc_start: 0.8292 (ppp) cc_final: 0.7961 (ppp)
REVERT: A 1113 MET cc_start: 0.8574 (ttp) cc_final: 0.7680 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0502
  time to fit residues: 15.3975
Evaluate side-chains
  172 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 48 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 363 ASN
A 858 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.144299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.121910 restraints weight = 13719.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.125837 restraints weight = 8224.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.128648 restraints weight = 5488.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.130549 restraints weight = 3938.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.131940 restraints weight = 3016.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.5297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6699  Z= 0.141
  Angle     :  0.720   9.647   9140  Z= 0.363
  Chirality :  0.044   0.193   1076
  Planarity :  0.004   0.049   1104
  Dihedral  :  7.594  57.414   1248
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.07 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 are not related in a simple way.
  whole: -1.64 (0.29), residues: 804
  helix:  0.49 (0.23), residues: 486
  sheet: -4.40 (0.90), residues: 18
  loop : -3.69 (0.31), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1068 
 TYR   0.028   0.002   TYR A1011 
 PHE   0.027   0.002   PHE A1111 
 TRP   0.021   0.001   TRP A 651 
 HIS   0.013   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6698)
  covalent geometry    : angle       0.71972 ( 9138)
  SS BOND              : bond        0.00194 (    1)
  SS BOND              : angle       0.98286 (    2)
  hydrogen bonds       : bond        0.04767 (  357)
  hydrogen bonds       : angle       4.57345 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9267 (tp) cc_final: 0.8948 (tp)
REVERT: A  383 ARG cc_start: 0.7833 (mtt180) cc_final: 0.6585 (tpp-160)
REVERT: A  453 MET cc_start: 0.4759 (pmm) cc_final: 0.4550 (pmm)
REVERT: A  465 MET cc_start: 0.8530 (ttt) cc_final: 0.7610 (tmm)
REVERT: A  518 MET cc_start: 0.8804 (ttm) cc_final: 0.8478 (ttm)
REVERT: A  536 ILE cc_start: 0.8940 (mm) cc_final: 0.8614 (mm)
REVERT: A  557 PHE cc_start: 0.9213 (p90) cc_final: 0.8967 (p90)
REVERT: A  581 TRP cc_start: 0.8877 (t-100) cc_final: 0.7957 (t-100)
REVERT: A  584 THR cc_start: 0.9561 (p) cc_final: 0.9220 (p)
REVERT: A  587 ASP cc_start: 0.8850 (p0) cc_final: 0.8068 (m-30)
REVERT: A  596 THR cc_start: 0.9402 (p) cc_final: 0.9101 (p)
REVERT: A  743 LYS cc_start: 0.8053 (ptmt) cc_final: 0.7494 (ptpt)
REVERT: A  765 ASP cc_start: 0.6866 (m-30) cc_final: 0.6494 (m-30)
REVERT: A  781 GLU cc_start: 0.8306 (tt0) cc_final: 0.7722 (tm-30)
REVERT: A  791 TRP cc_start: 0.8056 (m-10) cc_final: 0.7563 (m-10)
REVERT: A  796 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8365 (tm-30)
REVERT: A  798 ASN cc_start: 0.7863 (p0) cc_final: 0.7238 (t0)
REVERT: A  811 THR cc_start: 0.8217 (p) cc_final: 0.8006 (p)
REVERT: A  884 GLU cc_start: 0.6947 (mp0) cc_final: 0.6541 (tp30)
REVERT: A 1007 ILE cc_start: 0.8116 (tt) cc_final: 0.7324 (tp)
REVERT: A 1023 THR cc_start: 0.9337 (m) cc_final: 0.9056 (p)
REVERT: A 1113 MET cc_start: 0.8712 (ttp) cc_final: 0.7768 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0530
  time to fit residues: 16.2061
Evaluate side-chains
  168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 75 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 81 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0470
   chunk 56 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    2.1284

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 324 ASN
A 363 ASN
A 784 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.138032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.116569 restraints weight = 13892.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.119843 restraints weight = 8648.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.122489 restraints weight = 6047.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.124401 restraints weight = 4418.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.125646 restraints weight = 3404.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.5257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6699  Z= 0.188
  Angle     :  0.788   8.599   9140  Z= 0.402
  Chirality :  0.047   0.225   1076
  Planarity :  0.005   0.052   1104
  Dihedral  :  7.703  55.553   1248
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 11.19 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  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 are not related in a simple way.
  whole: -1.69 (0.29), residues: 804
  helix:  0.41 (0.23), residues: 482
  sheet: -3.90 (1.13), residues: 18
  loop : -3.60 (0.32), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1068 
 TYR   0.026   0.002   TYR A1011 
 PHE   0.027   0.002   PHE A1111 
 TRP   0.023   0.002   TRP A 826 
 HIS   0.010   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 6698)
  covalent geometry    : angle       0.78742 ( 9138)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       2.15319 (    2)
  hydrogen bonds       : bond        0.05444 (  357)
  hydrogen bonds       : angle       4.69429 ( 1071)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8988 (pp) cc_final: 0.8672 (pp)
REVERT: A  221 LEU cc_start: 0.9449 (tp) cc_final: 0.8883 (tp)
REVERT: A  233 ARG cc_start: 0.9016 (mtt180) cc_final: 0.8741 (mtt-85)
REVERT: A  383 ARG cc_start: 0.7835 (mtt180) cc_final: 0.6644 (tpt-90)
REVERT: A  465 MET cc_start: 0.8610 (ttt) cc_final: 0.7508 (tmm)
REVERT: A  466 ASN cc_start: 0.8181 (t0) cc_final: 0.7935 (t0)
REVERT: A  536 ILE cc_start: 0.9126 (mm) cc_final: 0.8779 (mm)
REVERT: A  578 CYS cc_start: 0.9359 (m) cc_final: 0.8872 (m)
REVERT: A  584 THR cc_start: 0.9511 (p) cc_final: 0.9122 (p)
REVERT: A  587 ASP cc_start: 0.8843 (p0) cc_final: 0.8033 (m-30)
REVERT: A  608 MET cc_start: 0.8931 (mtt) cc_final: 0.8473 (mtt)
REVERT: A  645 TYR cc_start: 0.9282 (t80) cc_final: 0.8923 (t80)
REVERT: A  791 TRP cc_start: 0.8110 (m-10) cc_final: 0.7625 (m-10)
REVERT: A  796 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8403 (tm-30)
REVERT: A  798 ASN cc_start: 0.7832 (p0) cc_final: 0.7080 (t0)
REVERT: A  811 THR cc_start: 0.8322 (p) cc_final: 0.8088 (p)
REVERT: A  884 GLU cc_start: 0.7050 (mp0) cc_final: 0.6282 (tp30)
REVERT: A  967 PHE cc_start: 0.9038 (t80) cc_final: 0.8800 (t80)
REVERT: A 1007 ILE cc_start: 0.8254 (tt) cc_final: 0.8044 (tp)
REVERT: A 1083 MET cc_start: 0.8776 (mmp) cc_final: 0.8313 (ttm)
REVERT: A 1113 MET cc_start: 0.8644 (ttp) cc_final: 0.7665 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0568
  time to fit residues: 16.1225
Evaluate side-chains
  163 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 363 ASN
** A 977 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 = 0.3683 r_free = 0.3683 target = 0.135334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.113682 restraints weight = 14033.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.117111 restraints weight = 8761.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.119617 restraints weight = 6016.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.121191 restraints weight = 4424.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.122681 restraints weight = 3498.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.5297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6699  Z= 0.203
  Angle     :  0.815  15.547   9140  Z= 0.415
  Chirality :  0.047   0.218   1076
  Planarity :  0.005   0.054   1104
  Dihedral  :  8.034  58.180   1248
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.82 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.30 %
    Favored  : 99.55 %
  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 are not related in a simple way.
  whole: -1.88 (0.28), residues: 804
  helix:  0.18 (0.22), residues: 492
  sheet: -3.34 (1.59), residues: 12
  loop : -3.74 (0.31), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 892 
 TYR   0.029   0.002   TYR A1011 
 PHE   0.048   0.003   PHE A1126 
 TRP   0.026   0.002   TRP A 826 
 HIS   0.012   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 6698)
  covalent geometry    : angle       0.81478 ( 9138)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       1.28579 (    2)
  hydrogen bonds       : bond        0.05627 (  357)
  hydrogen bonds       : angle       4.71640 ( 1071)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1022.07 seconds
wall clock time: 18 minutes 27.37 seconds (1107.37 seconds total)