Starting phenix.real_space_refine
on Tue Mar 11 22:46:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xe6_22144/03_2025/6xe6_22144.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xe6_22144/03_2025/6xe6_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_2025/6xe6_22144.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xe6_22144/03_2025/6xe6_22144.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xe6_22144/03_2025/6xe6_22144.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xe6_22144/03_2025/6xe6_22144.cif"
  }
  resolution = 4.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 3}
          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: 4.72, per 1000 atoms: 0.72
  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: 1.59
  Conformation dependent library (CDL) restraints added in 952.6 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: 0.54
  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: 1.65

  Time building geometry restraints manager: 1.92 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:             1.410
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.060
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.680
-------------------------------------------------------------------------------
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   6698  Z= 0.688
  Angle     :  1.399  10.649   9138  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 : 10.14
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.019   0.002   TRP A 826 
 HIS   0.017   0.002   HIS A 876 
 PHE   0.024   0.003   PHE A 839 
 TYR   0.019   0.002   TYR A 764 
 ARG   0.010   0.001   ARG A1078 

*********************** 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  : 0.683 
Fit side-chains
REVERT: A  220 LEU cc_start: 0.9012 (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: 0.7709 (m-30) cc_final: 0.7436 (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: 0.7961 (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: 0.8595 (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: 0.8158 (m-80)
REVERT: A  796 GLU cc_start: 0.8965 (tt0) cc_final: 0.8686 (tt0)
REVERT: A  798 ASN cc_start: 0.7981 (p0) cc_final: 0.7290 (t0)
REVERT: A  889 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8387 (m)
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: 0.8249 (m-80) cc_final: 0.8013 (m-80)
REVERT: A 1083 MET cc_start: 0.8866 (mmp) cc_final: 0.8645 (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: 0.7541 (ppp)
  outliers start: 7
  outliers final: 2
  residues processed: 236
  average time/residue: 0.1581
  time to fit residues: 51.4363
Evaluate side-chains
  189 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 185
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 62 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
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 778 HIS
A 941 HIS
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.131256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.109273 restraints weight = 14195.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112396 restraints weight = 8897.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.114935 restraints weight = 6278.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076   6698  Z= 0.329
  Angle     :  0.823   8.902   9138  Z= 0.427
  Chirality :  0.048   0.228   1076
  Planarity :  0.005   0.038   1104
  Dihedral  :  8.968  56.568   1248
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.70 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  4.66 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.27), residues: 804
  helix: -0.66 (0.22), residues: 491
  sheet:  None (None), residues: 0
  loop : -4.38 (0.28), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 826 
 HIS   0.006   0.001   HIS A 429 
 PHE   0.032   0.003   PHE A 725 
 TYR   0.036   0.002   TYR A1011 
 ARG   0.004   0.001   ARG A1132 

*********************** 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
  213 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 211
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9386 (tp) cc_final: 0.9000 (tp)
REVERT: A  302 ARG cc_start: 0.7318 (ptt-90) cc_final: 0.7023 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7801 (mtt180) cc_final: 0.6555 (tpt-90)
REVERT: A  453 MET cc_start: 0.5462 (pmm) cc_final: 0.5178 (pmm)
REVERT: A  465 MET cc_start: 0.8428 (ttt) cc_final: 0.7980 (tpp)
REVERT: A  489 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7047 (p90)
REVERT: A  540 ILE cc_start: 0.9305 (pt) cc_final: 0.9077 (tp)
REVERT: A  573 ASP cc_start: 0.8790 (m-30) cc_final: 0.8378 (m-30)
REVERT: A  578 CYS cc_start: 0.9432 (m) cc_final: 0.9088 (m)
REVERT: A  581 TRP cc_start: 0.8962 (t-100) cc_final: 0.7997 (t-100)
REVERT: A  596 THR cc_start: 0.9353 (p) cc_final: 0.9150 (p)
REVERT: A  597 VAL cc_start: 0.9736 (p) cc_final: 0.9388 (p)
REVERT: A  636 TYR cc_start: 0.8878 (t80) cc_final: 0.8619 (t80)
REVERT: A  725 PHE cc_start: 0.8535 (t80) cc_final: 0.8148 (t80)
REVERT: A  738 ILE cc_start: 0.7294 (mt) cc_final: 0.7038 (mt)
REVERT: A  781 GLU cc_start: 0.8352 (tt0) cc_final: 0.7778 (tp30)
REVERT: A  796 GLU cc_start: 0.8880 (tt0) cc_final: 0.8170 (tm-30)
REVERT: A  798 ASN cc_start: 0.8004 (p0) cc_final: 0.7217 (t0)
REVERT: A  927 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8907 (m-10)
REVERT: A  950 TRP cc_start: 0.8767 (t-100) cc_final: 0.8470 (t-100)
REVERT: A 1033 GLU cc_start: 0.8984 (pm20) cc_final: 0.8765 (pm20)
REVERT: A 1043 SER cc_start: 0.9433 (m) cc_final: 0.9116 (t)
REVERT: A 1112 MET cc_start: 0.8405 (ppp) cc_final: 0.7960 (ppp)
  outliers start: 2
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1473
  time to fit residues: 44.5940
Evaluate side-chains
  169 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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**
** A1128 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.138377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.115882 restraints weight = 13831.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.119501 restraints weight = 8292.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.122069 restraints weight = 5579.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6698  Z= 0.207
  Angle     :  0.719  11.375   9138  Z= 0.369
  Chirality :  0.044   0.187   1076
  Planarity :  0.004   0.037   1104
  Dihedral  :  8.308  52.698   1248
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.32 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.81 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.28), residues: 804
  helix:  0.01 (0.23), residues: 488
  sheet:  None (None), residues: 0
  loop : -4.16 (0.29), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 826 
 HIS   0.008   0.001   HIS A 590 
 PHE   0.027   0.002   PHE A 839 
 TYR   0.015   0.002   TYR A1011 
 ARG   0.001   0.000   ARG A 233 

*********************** 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
  210 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 ASP cc_start: 0.8994 (t0) cc_final: 0.8756 (t0)
REVERT: A  220 LEU cc_start: 0.8789 (pp) cc_final: 0.8437 (pp)
REVERT: A  221 LEU cc_start: 0.9320 (tp) cc_final: 0.8836 (tp)
REVERT: A  233 ARG cc_start: 0.8907 (mtt180) cc_final: 0.8110 (mtt-85)
REVERT: A  302 ARG cc_start: 0.7312 (ptt-90) cc_final: 0.6977 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7896 (mtt180) cc_final: 0.6576 (tpt-90)
REVERT: A  453 MET cc_start: 0.4887 (pmm) cc_final: 0.3655 (pmm)
REVERT: A  465 MET cc_start: 0.8363 (ttt) cc_final: 0.7929 (tmm)
REVERT: A  536 ILE cc_start: 0.9164 (mm) cc_final: 0.8858 (mm)
REVERT: A  573 ASP cc_start: 0.8695 (m-30) cc_final: 0.8443 (m-30)
REVERT: A  578 CYS cc_start: 0.9421 (m) cc_final: 0.9156 (m)
REVERT: A  581 TRP cc_start: 0.8851 (t-100) cc_final: 0.7808 (t-100)
REVERT: A  584 THR cc_start: 0.9598 (p) cc_final: 0.9241 (p)
REVERT: A  587 ASP cc_start: 0.8805 (p0) cc_final: 0.8246 (m-30)
REVERT: A  596 THR cc_start: 0.9392 (p) cc_final: 0.9073 (p)
REVERT: A  597 VAL cc_start: 0.9714 (p) cc_final: 0.9471 (p)
REVERT: A  636 TYR cc_start: 0.8709 (t80) cc_final: 0.8422 (t80)
REVERT: A  645 TYR cc_start: 0.9446 (t80) cc_final: 0.9211 (t80)
REVERT: A  725 PHE cc_start: 0.8367 (t80) cc_final: 0.7816 (t80)
REVERT: A  796 GLU cc_start: 0.8922 (tt0) cc_final: 0.7965 (tm-30)
REVERT: A  798 ASN cc_start: 0.7878 (p0) cc_final: 0.7138 (t0)
REVERT: A  895 MET cc_start: -0.0360 (mmt) cc_final: -0.1266 (mtp)
REVERT: A  972 GLU cc_start: 0.8699 (tt0) cc_final: 0.8314 (tt0)
REVERT: A 1083 MET cc_start: 0.8925 (mmp) cc_final: 0.8394 (mmp)
REVERT: A 1112 MET cc_start: 0.8551 (ppp) cc_final: 0.8113 (ppp)
REVERT: A 1113 MET cc_start: 0.8709 (ttp) cc_final: 0.7765 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 210
  average time/residue: 0.1365
  time to fit residues: 40.9001
Evaluate side-chains
  166 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 644 ASN
A 837 GLN
** A1128 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 = 0.3746 r_free = 0.3746 target = 0.139494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.118102 restraints weight = 14425.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.121322 restraints weight = 9092.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.123641 restraints weight = 6291.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6698  Z= 0.193
  Angle     :  0.684   7.975   9138  Z= 0.355
  Chirality :  0.043   0.174   1076
  Planarity :  0.004   0.041   1104
  Dihedral  :  8.048  59.518   1248
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.33 %
    Favored  : 90.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.29), residues: 804
  helix:  0.16 (0.23), residues: 490
  sheet: -5.26 (0.56), residues: 16
  loop : -3.99 (0.30), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1032 
 HIS   0.011   0.001   HIS A 429 
 PHE   0.020   0.002   PHE A 725 
 TYR   0.036   0.002   TYR A1011 
 ARG   0.001   0.000   ARG A 547 

*********************** 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
  211 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8788 (pp) cc_final: 0.8433 (pp)
REVERT: A  221 LEU cc_start: 0.9392 (tp) cc_final: 0.8911 (tp)
REVERT: A  233 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8765 (mtt-85)
REVERT: A  383 ARG cc_start: 0.7795 (mtt180) cc_final: 0.6569 (tpt-90)
REVERT: A  453 MET cc_start: 0.5171 (pmm) cc_final: 0.3877 (pmm)
REVERT: A  465 MET cc_start: 0.8249 (ttt) cc_final: 0.8005 (tmm)
REVERT: A  530 MET cc_start: 0.9363 (tpt) cc_final: 0.9126 (tpt)
REVERT: A  536 ILE cc_start: 0.9109 (mm) cc_final: 0.8779 (mm)
REVERT: A  557 PHE cc_start: 0.9166 (p90) cc_final: 0.8862 (p90)
REVERT: A  578 CYS cc_start: 0.9358 (m) cc_final: 0.8950 (m)
REVERT: A  581 TRP cc_start: 0.8784 (t-100) cc_final: 0.8545 (t-100)
REVERT: A  587 ASP cc_start: 0.8751 (p0) cc_final: 0.8080 (m-30)
REVERT: A  608 MET cc_start: 0.8882 (mtt) cc_final: 0.8582 (mtt)
REVERT: A  645 TYR cc_start: 0.9367 (t80) cc_final: 0.9103 (t80)
REVERT: A  796 GLU cc_start: 0.8775 (tt0) cc_final: 0.7977 (tm-30)
REVERT: A  798 ASN cc_start: 0.7745 (p0) cc_final: 0.6898 (t0)
REVERT: A  811 THR cc_start: 0.8075 (p) cc_final: 0.7724 (p)
REVERT: A  970 ASN cc_start: 0.8293 (p0) cc_final: 0.8077 (p0)
REVERT: A 1083 MET cc_start: 0.9150 (mmp) cc_final: 0.8193 (ttm)
REVERT: A 1112 MET cc_start: 0.8558 (ppp) cc_final: 0.7783 (ppp)
REVERT: A 1113 MET cc_start: 0.8551 (ttp) cc_final: 0.7598 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.1317
  time to fit residues: 39.7345
Evaluate side-chains
  167 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    0.0970
   chunk 20 optimal weight:   10.0000
   chunk 33 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0470
   chunk 73 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.5076

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

Flipped N/Q/H residues before XYZ refinement:
A 590 HIS
A 858 GLN
** A1128 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 = 0.3794 r_free = 0.3794 target = 0.143838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.122570 restraints weight = 14243.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.125405 restraints weight = 9423.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.127509 restraints weight = 6773.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6698  Z= 0.189
  Angle     :  0.684   7.534   9138  Z= 0.353
  Chirality :  0.043   0.193   1076
  Planarity :  0.004   0.040   1104
  Dihedral  :  7.967  58.521   1248
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.45 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.30), residues: 804
  helix:  0.42 (0.23), residues: 482
  sheet: -5.00 (0.63), residues: 16
  loop : -3.70 (0.32), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 791 
 HIS   0.012   0.001   HIS A 429 
 PHE   0.022   0.002   PHE A 879 
 TYR   0.038   0.002   TYR A1011 
 ARG   0.001   0.000   ARG A1132 

*********************** 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
  206 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9294 (tp) cc_final: 0.9041 (tp)
REVERT: A  228 THR cc_start: 0.8927 (p) cc_final: 0.8449 (p)
REVERT: A  302 ARG cc_start: 0.7177 (ptt-90) cc_final: 0.6800 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7698 (mtt180) cc_final: 0.6501 (tpt-90)
REVERT: A  453 MET cc_start: 0.4986 (pmm) cc_final: 0.4631 (pmm)
REVERT: A  465 MET cc_start: 0.8209 (ttt) cc_final: 0.7750 (tmm)
REVERT: A  487 ILE cc_start: 0.7425 (tp) cc_final: 0.7220 (tt)
REVERT: A  530 MET cc_start: 0.9213 (tpt) cc_final: 0.8894 (tpp)
REVERT: A  536 ILE cc_start: 0.8955 (mm) cc_final: 0.8583 (mm)
REVERT: A  564 ILE cc_start: 0.9501 (mm) cc_final: 0.9280 (mm)
REVERT: A  578 CYS cc_start: 0.9267 (m) cc_final: 0.8836 (m)
REVERT: A  581 TRP cc_start: 0.8708 (t-100) cc_final: 0.7707 (t-100)
REVERT: A  584 THR cc_start: 0.9512 (p) cc_final: 0.9206 (p)
REVERT: A  587 ASP cc_start: 0.8724 (p0) cc_final: 0.8021 (m-30)
REVERT: A  596 THR cc_start: 0.9301 (p) cc_final: 0.8961 (p)
REVERT: A  597 VAL cc_start: 0.9586 (p) cc_final: 0.9309 (p)
REVERT: A  608 MET cc_start: 0.8708 (mtt) cc_final: 0.8503 (mtt)
REVERT: A  645 TYR cc_start: 0.9344 (t80) cc_final: 0.8962 (t80)
REVERT: A  725 PHE cc_start: 0.8089 (t80) cc_final: 0.7854 (t80)
REVERT: A  742 MET cc_start: 0.6511 (ttp) cc_final: 0.6186 (tmm)
REVERT: A  796 GLU cc_start: 0.8647 (tt0) cc_final: 0.7987 (tm-30)
REVERT: A  798 ASN cc_start: 0.7472 (p0) cc_final: 0.6571 (t0)
REVERT: A  810 LEU cc_start: 0.8889 (pt) cc_final: 0.8505 (pp)
REVERT: A  895 MET cc_start: -0.0652 (mmt) cc_final: -0.1402 (mtp)
REVERT: A 1007 ILE cc_start: 0.8631 (tt) cc_final: 0.8121 (tp)
REVERT: A 1083 MET cc_start: 0.9009 (mmp) cc_final: 0.8339 (ttm)
REVERT: A 1112 MET cc_start: 0.8324 (ppp) cc_final: 0.7827 (ppp)
REVERT: A 1113 MET cc_start: 0.8340 (ttp) cc_final: 0.7535 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1369
  time to fit residues: 40.5119
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  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 7 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    0.2980
   chunk 75 optimal weight:    2.9990
   chunk 50 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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
** A1128 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 = 0.3783 r_free = 0.3783 target = 0.142381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.121191 restraints weight = 14264.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.123997 restraints weight = 9478.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.126023 restraints weight = 6834.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.4773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6698  Z= 0.196
  Angle     :  0.694   8.533   9138  Z= 0.360
  Chirality :  0.044   0.168   1076
  Planarity :  0.004   0.043   1104
  Dihedral  :  7.900  59.918   1248
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.58 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.29), residues: 804
  helix:  0.37 (0.23), residues: 485
  sheet: -4.77 (0.74), residues: 16
  loop : -3.68 (0.32), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 791 
 HIS   0.011   0.001   HIS A 429 
 PHE   0.020   0.002   PHE A 725 
 TYR   0.055   0.002   TYR A1011 
 ARG   0.001   0.000   ARG A1132 

*********************** 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
  204 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8847 (pp) cc_final: 0.8481 (pp)
REVERT: A  221 LEU cc_start: 0.9302 (tp) cc_final: 0.8728 (tp)
REVERT: A  302 ARG cc_start: 0.7278 (ptt-90) cc_final: 0.6942 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7749 (mtt180) cc_final: 0.6558 (tpp-160)
REVERT: A  465 MET cc_start: 0.8513 (ttt) cc_final: 0.7556 (tmm)
REVERT: A  530 MET cc_start: 0.9239 (tpt) cc_final: 0.8951 (tpp)
REVERT: A  578 CYS cc_start: 0.9294 (m) cc_final: 0.8884 (m)
REVERT: A  581 TRP cc_start: 0.8751 (t-100) cc_final: 0.8461 (t-100)
REVERT: A  645 TYR cc_start: 0.9381 (t80) cc_final: 0.9141 (t80)
REVERT: A  725 PHE cc_start: 0.8244 (t80) cc_final: 0.7788 (t80)
REVERT: A  798 ASN cc_start: 0.7657 (p0) cc_final: 0.6842 (t0)
REVERT: A  810 LEU cc_start: 0.8818 (pt) cc_final: 0.8539 (pp)
REVERT: A 1083 MET cc_start: 0.9145 (mmp) cc_final: 0.8399 (ttm)
REVERT: A 1112 MET cc_start: 0.8320 (ppp) cc_final: 0.8003 (ppp)
REVERT: A 1113 MET cc_start: 0.8487 (ttp) cc_final: 0.7685 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1276
  time to fit residues: 37.3446
Evaluate side-chains
  164 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 59 optimal weight:    0.4980
   chunk 63 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0980
   chunk 1 optimal weight:    0.4980
   chunk 6 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 356 ASN
A 363 ASN
A 858 GLN
** A1128 GLN ** 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 = 0.3832 r_free = 0.3832 target = 0.146369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.124353 restraints weight = 13707.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.127610 restraints weight = 8736.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.129999 restraints weight = 6115.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6698  Z= 0.179
  Angle     :  0.706   8.425   9138  Z= 0.358
  Chirality :  0.044   0.211   1076
  Planarity :  0.004   0.045   1104
  Dihedral  :  7.635  59.534   1248
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.70 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.29), residues: 804
  helix:  0.45 (0.23), residues: 486
  sheet: -4.19 (1.22), residues: 10
  loop : -3.75 (0.30), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 791 
 HIS   0.012   0.001   HIS A 429 
 PHE   0.017   0.002   PHE A 725 
 TYR   0.030   0.001   TYR A1011 
 ARG   0.002   0.000   ARG A 233 

*********************** 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
  200 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8709 (pp) cc_final: 0.8469 (pp)
REVERT: A  221 LEU cc_start: 0.9294 (tp) cc_final: 0.8954 (tp)
REVERT: A  383 ARG cc_start: 0.7727 (mtt180) cc_final: 0.6529 (tpp-160)
REVERT: A  465 MET cc_start: 0.8364 (ttt) cc_final: 0.7724 (tmm)
REVERT: A  518 MET cc_start: 0.8593 (ttm) cc_final: 0.8210 (tpp)
REVERT: A  536 ILE cc_start: 0.8887 (mm) cc_final: 0.8524 (mm)
REVERT: A  558 MET cc_start: 0.9225 (mpp) cc_final: 0.8879 (mpp)
REVERT: A  584 THR cc_start: 0.9560 (p) cc_final: 0.9227 (p)
REVERT: A  587 ASP cc_start: 0.8709 (p0) cc_final: 0.8247 (m-30)
REVERT: A  645 TYR cc_start: 0.9334 (t80) cc_final: 0.9029 (t80)
REVERT: A  725 PHE cc_start: 0.8434 (t80) cc_final: 0.7796 (t80)
REVERT: A  781 GLU cc_start: 0.8342 (tt0) cc_final: 0.7691 (tp30)
REVERT: A  798 ASN cc_start: 0.8020 (p0) cc_final: 0.6648 (t0)
REVERT: A  811 THR cc_start: 0.7982 (p) cc_final: 0.7627 (p)
REVERT: A  824 GLN cc_start: 0.8308 (pp30) cc_final: 0.7763 (pm20)
REVERT: A  888 LEU cc_start: 0.8197 (mp) cc_final: 0.7919 (tp)
REVERT: A 1083 MET cc_start: 0.9119 (mmp) cc_final: 0.8365 (ttm)
REVERT: A 1112 MET cc_start: 0.8306 (ppp) cc_final: 0.8032 (ppp)
REVERT: A 1113 MET cc_start: 0.8561 (ttp) cc_final: 0.7762 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1304
  time to fit residues: 37.2634
Evaluate side-chains
  161 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 837 GLN
** A1128 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 = 0.3821 r_free = 0.3821 target = 0.145757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.122855 restraints weight = 13713.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.126581 restraints weight = 8528.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.129189 restraints weight = 5835.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.5318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6698  Z= 0.185
  Angle     :  0.704   8.355   9138  Z= 0.360
  Chirality :  0.044   0.212   1076
  Planarity :  0.005   0.046   1104
  Dihedral  :  7.609  58.085   1248
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.45 %
    Favored  : 90.05 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.29), residues: 804
  helix:  0.37 (0.23), residues: 490
  sheet: -4.32 (0.99), residues: 16
  loop : -3.87 (0.30), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 950 
 HIS   0.012   0.001   HIS A 429 
 PHE   0.014   0.002   PHE A 886 
 TYR   0.025   0.002   TYR A1011 
 ARG   0.003   0.000   ARG A 302 

*********************** 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
  193 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9314 (tp) cc_final: 0.8989 (tp)
REVERT: A  383 ARG cc_start: 0.7802 (mtt180) cc_final: 0.6622 (tpt170)
REVERT: A  465 MET cc_start: 0.8365 (ttt) cc_final: 0.7752 (tmm)
REVERT: A  518 MET cc_start: 0.8716 (ttm) cc_final: 0.8288 (tpp)
REVERT: A  557 PHE cc_start: 0.9232 (p90) cc_final: 0.8949 (p90)
REVERT: A  584 THR cc_start: 0.9524 (p) cc_final: 0.9205 (p)
REVERT: A  587 ASP cc_start: 0.8679 (p0) cc_final: 0.8236 (m-30)
REVERT: A  645 TYR cc_start: 0.9353 (t80) cc_final: 0.9060 (t80)
REVERT: A  725 PHE cc_start: 0.8429 (t80) cc_final: 0.7925 (t80)
REVERT: A  742 MET cc_start: 0.6463 (tmm) cc_final: 0.6208 (tmm)
REVERT: A  781 GLU cc_start: 0.8305 (tt0) cc_final: 0.7586 (tp30)
REVERT: A  796 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8330 (tm-30)
REVERT: A  798 ASN cc_start: 0.7861 (p0) cc_final: 0.7077 (t0)
REVERT: A  811 THR cc_start: 0.7943 (p) cc_final: 0.7714 (p)
REVERT: A  824 GLN cc_start: 0.8268 (pp30) cc_final: 0.7787 (pm20)
REVERT: A 1083 MET cc_start: 0.8830 (mmp) cc_final: 0.8299 (ttm)
REVERT: A 1096 MET cc_start: 0.8615 (ttt) cc_final: 0.8396 (ttp)
REVERT: A 1112 MET cc_start: 0.8303 (ppp) cc_final: 0.8033 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1436
  time to fit residues: 39.5206
Evaluate side-chains
  161 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 79 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
A 363 ASN
A 858 GLN
** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.144766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.121750 restraints weight = 13601.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.125664 restraints weight = 8262.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.128466 restraints weight = 5566.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.5451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6698  Z= 0.192
  Angle     :  0.711   9.364   9138  Z= 0.363
  Chirality :  0.044   0.224   1076
  Planarity :  0.005   0.048   1104
  Dihedral  :  7.512  59.278   1248
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.32 %
    Favored  : 89.30 %
  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 : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.29), residues: 804
  helix:  0.42 (0.23), residues: 490
  sheet: -4.51 (0.96), residues: 18
  loop : -3.92 (0.29), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 791 
 HIS   0.005   0.001   HIS A1055 
 PHE   0.020   0.002   PHE A 839 
 TYR   0.024   0.002   TYR A1011 
 ARG   0.002   0.000   ARG A 302 

*********************** 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
  196 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9318 (tp) cc_final: 0.8988 (tp)
REVERT: A  233 ARG cc_start: 0.9006 (mtt180) cc_final: 0.8777 (mtt-85)
REVERT: A  377 HIS cc_start: 0.8615 (m170) cc_final: 0.8172 (p-80)
REVERT: A  383 ARG cc_start: 0.7809 (mtt180) cc_final: 0.6660 (tpt170)
REVERT: A  453 MET cc_start: 0.4558 (pmm) cc_final: 0.3645 (pmm)
REVERT: A  465 MET cc_start: 0.8357 (ttt) cc_final: 0.7740 (tmm)
REVERT: A  518 MET cc_start: 0.8802 (ttm) cc_final: 0.8236 (tpp)
REVERT: A  558 MET cc_start: 0.9264 (mpp) cc_final: 0.8878 (mpp)
REVERT: A  584 THR cc_start: 0.9508 (p) cc_final: 0.9118 (p)
REVERT: A  587 ASP cc_start: 0.8640 (p0) cc_final: 0.8229 (m-30)
REVERT: A  645 TYR cc_start: 0.9387 (t80) cc_final: 0.9118 (t80)
REVERT: A  742 MET cc_start: 0.6400 (tmm) cc_final: 0.6135 (tmm)
REVERT: A  781 GLU cc_start: 0.8299 (tt0) cc_final: 0.7562 (tp30)
REVERT: A  796 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8291 (tm-30)
REVERT: A  798 ASN cc_start: 0.7873 (p0) cc_final: 0.7096 (t0)
REVERT: A  811 THR cc_start: 0.8040 (p) cc_final: 0.7781 (p)
REVERT: A  824 GLN cc_start: 0.8374 (pp30) cc_final: 0.8038 (tm-30)
REVERT: A  884 GLU cc_start: 0.7384 (tp30) cc_final: 0.7034 (mp0)
REVERT: A 1083 MET cc_start: 0.9148 (mmp) cc_final: 0.8296 (ttm)
REVERT: A 1112 MET cc_start: 0.8252 (ppp) cc_final: 0.8016 (ppp)
REVERT: A 1113 MET cc_start: 0.8638 (ttp) cc_final: 0.7778 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.1477
  time to fit residues: 41.0505
Evaluate side-chains
  166 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 79 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 35 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
A 356 ASN
A 363 ASN
A 659 HIS
** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1128 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.146372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.123549 restraints weight = 13591.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.127277 restraints weight = 8490.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.129880 restraints weight = 5833.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.5679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6698  Z= 0.181
  Angle     :  0.713  10.170   9138  Z= 0.363
  Chirality :  0.044   0.217   1076
  Planarity :  0.005   0.050   1104
  Dihedral  :  7.339  58.298   1248
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.45 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.29), residues: 804
  helix:  0.44 (0.24), residues: 484
  sheet: -3.86 (1.19), residues: 16
  loop : -3.84 (0.29), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 651 
 HIS   0.004   0.001   HIS A 659 
 PHE   0.048   0.002   PHE A1126 
 TYR   0.023   0.002   TYR A1011 
 ARG   0.002   0.000   ARG A 302 

********************** 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
  196 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 LEU cc_start: 0.8364 (mm) cc_final: 0.8111 (tp)
REVERT: A  220 LEU cc_start: 0.8768 (pp) cc_final: 0.8459 (pp)
REVERT: A  221 LEU cc_start: 0.9337 (tp) cc_final: 0.8724 (tp)
REVERT: A  377 HIS cc_start: 0.8575 (m170) cc_final: 0.8176 (p-80)
REVERT: A  383 ARG cc_start: 0.7729 (mtt180) cc_final: 0.6567 (tpp-160)
REVERT: A  453 MET cc_start: 0.4198 (pmm) cc_final: 0.3446 (pmm)
REVERT: A  465 MET cc_start: 0.8327 (ttt) cc_final: 0.7711 (tmm)
REVERT: A  518 MET cc_start: 0.8749 (ttm) cc_final: 0.8206 (tpp)
REVERT: A  558 MET cc_start: 0.9283 (mpp) cc_final: 0.8935 (mpp)
REVERT: A  584 THR cc_start: 0.9520 (p) cc_final: 0.9138 (p)
REVERT: A  587 ASP cc_start: 0.8665 (p0) cc_final: 0.8167 (m-30)
REVERT: A  645 TYR cc_start: 0.9362 (t80) cc_final: 0.9090 (t80)
REVERT: A  742 MET cc_start: 0.6364 (tmm) cc_final: 0.6110 (tmm)
REVERT: A  781 GLU cc_start: 0.8289 (tt0) cc_final: 0.7593 (tp30)
REVERT: A  796 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8319 (tm-30)
REVERT: A  798 ASN cc_start: 0.7763 (p0) cc_final: 0.6958 (t0)
REVERT: A  811 THR cc_start: 0.7969 (p) cc_final: 0.7718 (p)
REVERT: A  824 GLN cc_start: 0.8311 (pp30) cc_final: 0.8032 (tm-30)
REVERT: A 1083 MET cc_start: 0.9147 (mmp) cc_final: 0.8511 (ttm)
REVERT: A 1113 MET cc_start: 0.8500 (ttp) cc_final: 0.7683 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.1510
  time to fit residues: 41.5522
Evaluate side-chains
  159 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 10 optimal weight:    7.9990
   chunk 44 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0370
   chunk 80 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8060

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

Flipped N/Q/H residues before XYZ refinement:
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.146857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123342 restraints weight = 13894.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.127249 restraints weight = 8465.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.130049 restraints weight = 5722.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.5763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6698  Z= 0.186
  Angle     :  0.729   9.390   9138  Z= 0.370
  Chirality :  0.045   0.233   1076
  Planarity :  0.005   0.053   1104
  Dihedral  :  7.314  58.044   1248
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.20 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.29), residues: 804
  helix:  0.41 (0.23), residues: 490
  sheet: -3.99 (1.19), residues: 18
  loop : -3.80 (0.30), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 651 
 HIS   0.013   0.001   HIS A 429 
 PHE   0.033   0.002   PHE A1126 
 TYR   0.023   0.002   TYR A 430 
 ARG   0.003   0.000   ARG A 302 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2082.94 seconds
wall clock time: 37 minutes 9.06 seconds (2229.06 seconds total)