Starting phenix.real_space_refine
on Fri Jul 25 05:03:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgj_50408/07_2025/9fgj_50408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgj_50408/07_2025/9fgj_50408.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fgj_50408/07_2025/9fgj_50408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgj_50408/07_2025/9fgj_50408.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgj_50408/07_2025/9fgj_50408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgj_50408/07_2025/9fgj_50408.cif"
  }
  resolution = 3.8
  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=   0.031
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      26      5.16       5
     C    4431      2.51       5
     N    1210      2.21       5
     O    1354      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7021
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 885, 7021
          Classifications: {'peptide': 885}
          Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 838}
          Chain breaks: 1
  Time building chain proxies: 4.57, per 1000 atoms: 0.65
  Number of scatterers: 7021
  At special positions: 0
  Unit cell: (95.853, 118.47, 112.008, 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      26     16.00
     O    1354      8.00
     N    1210      7.00
     C    4431      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 559 " - pdb=" SG  CYS A 566 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.77
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1678

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 4 sheets defined
      62.6% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.538A  pdb=" N   ASN A 236 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 251
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 283 through 308
    Processing helix  chain 'A' and resid 319 through 323
      removed outlier: 3.714A  pdb=" N   VAL A 323 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 336
    Processing helix  chain 'A' and resid 356 through 376
      removed outlier: 3.523A  pdb=" N   GLU A 360 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 398
      removed outlier: 3.520A  pdb=" N   VAL A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ASP A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 421
      removed outlier: 4.037A  pdb=" N   GLY A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 443
      removed outlier: 4.046A  pdb=" N   GLY A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   THR A 441 " --> pdb=" O   THR A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 462
      removed outlier: 3.862A  pdb=" N   LEU A 451 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 505
    Processing helix  chain 'A' and resid 523 through 529
    Processing helix  chain 'A' and resid 530 through 537
    Processing helix  chain 'A' and resid 538 through 541
      removed outlier: 4.276A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 538 through 541'
    Processing helix  chain 'A' and resid 546 through 551
      removed outlier: 3.862A  pdb=" N   TYR A 550 " --> pdb=" O   ALA A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'A' and resid 562 through 586
      removed outlier: 3.933A  pdb=" N   CYS A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A 582 " --> pdb=" O   GLN A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 614
      removed outlier: 3.967A  pdb=" N   ASN A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 642
      removed outlier: 3.629A  pdb=" N   PHE A 635 " --> pdb=" O   GLU A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 651
      removed outlier: 3.618A  pdb=" N   LEU A 651 " --> pdb=" O   VAL A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 666
      removed outlier: 3.684A  pdb=" N   ASP A 660 " --> pdb=" O   ILE A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 690
    Processing helix  chain 'A' and resid 697 through 711
      removed outlier: 3.543A  pdb=" N   ASN A 711 " --> pdb=" O   PHE A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 723
    Processing helix  chain 'A' and resid 731 through 753
      removed outlier: 3.512A  pdb=" N   VAL A 735 " --> pdb=" O   ASN A 731 " (cutoff:3.500A)
      Proline residue:  A 743  - end of helix
      removed outlier: 4.517A  pdb=" N   SER A 753 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 786
      removed outlier: 3.685A  pdb=" N   LYS A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 806
    Processing helix  chain 'A' and resid 807 through 812
    Processing helix  chain 'A' and resid 821 through 828
      removed outlier: 3.921A  pdb=" N   LEU A 825 " --> pdb=" O   ASN A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 901
    Processing helix  chain 'A' and resid 909 through 931
      removed outlier: 3.782A  pdb=" N   PHE A 913 " --> pdb=" O   ALA A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1052
    Processing helix  chain 'A' and resid 1052 through 1067
    Processing helix  chain 'A' and resid 1068 through 1079
    Processing helix  chain 'A' and resid 1081 through 1088
      removed outlier: 3.601A  pdb=" N   VAL A1088 " --> pdb=" O   GLU A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1092 through 1115
      Proline residue:  A1112  - end of helix
      removed outlier: 3.625A  pdb=" N   ARG A1115 " --> pdb=" O   GLU A1111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1124 through 1149
      removed outlier: 3.616A  pdb=" N   ILE A1149 " --> pdb=" O   ASP A1145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1153 through 1182
    Processing helix  chain 'A' and resid 1191 through 1214
      Proline residue:  A1209  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 493
    Processing sheet with id=AA2, first strand: chain 'A' and resid 623 through 625
    Processing sheet with id=AA3, first strand: chain 'A' and resid 760 through 765
      removed outlier: 6.878A  pdb=" N   ILE A 834 " --> pdb=" O   PHE A 890 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   LEU A 892 " --> pdb=" O   ILE A 834 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   GLU A 836 " --> pdb=" O   LEU A 892 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   ALA A 894 " --> pdb=" O   GLU A 836 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LEU A 838 " --> pdb=" O   ALA A 894 " (cutoff:3.500A)
      removed outlier: 9.293A  pdb=" N   LYS A 896 " --> pdb=" O   LEU A 838 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLY A 879 " --> pdb=" O   ARG A 887 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ILE A 889 " --> pdb=" O   LEU A 877 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   LEU A 877 " --> pdb=" O   ILE A 889 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   THR A 891 " --> pdb=" O   VAL A 875 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL A 875 " --> pdb=" O   THR A 891 " (cutoff:3.500A)
      removed outlier: 8.473A  pdb=" N   VAL A 893 " --> pdb=" O   THR A 873 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   THR A 873 " --> pdb=" O   VAL A 893 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   VAL A 895 " --> pdb=" O   VAL A 871 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   VAL A 871 " --> pdb=" O   VAL A 895 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 818

    384 hydrogen bonds defined for protein.
    1104 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: 1.95

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2357
        1.35 -     1.47: 1442
        1.47 -     1.59: 3307
        1.59 -     1.71: 0
        1.71 -     1.83: 45
  Bond restraints: 7151
  Sorted by residual:
  bond pdb=" N   ASN A 598 "
       pdb=" CA  ASN A 598 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.31e-02 5.83e+03 7.18e+00
  bond pdb=" N   ASP A 517 "
       pdb=" CA  ASP A 517 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.25e+00
  bond pdb=" N   MET A 599 "
       pdb=" CA  MET A 599 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.25e+00
  bond pdb=" C   GLN A 596 "
       pdb=" N   PRO A 597 "
    ideal  model  delta    sigma   weight residual
    1.332  1.360 -0.028 1.34e-02 5.57e+03 4.31e+00
  bond pdb=" CB  PRO A 615 "
       pdb=" CG  PRO A 615 "
    ideal  model  delta    sigma   weight residual
    1.492  1.566 -0.074 5.00e-02 4.00e+02 2.18e+00
  ... (remaining 7146 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 9540
        2.35 -     4.70: 104
        4.70 -     7.04: 14
        7.04 -     9.39: 3
        9.39 -    11.74: 1
  Bond angle restraints: 9662
  Sorted by residual:
  angle pdb=" CB  MET A 644 "
        pdb=" CG  MET A 644 "
        pdb=" SD  MET A 644 "
      ideal   model   delta    sigma   weight residual
     112.70  124.44  -11.74 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" N   PRO A 597 "
        pdb=" CA  PRO A 597 "
        pdb=" C   PRO A 597 "
      ideal   model   delta    sigma   weight residual
     111.21  116.96   -5.75 1.59e+00 3.96e-01 1.31e+01
  angle pdb=" CA  MET A1048 "
        pdb=" CB  MET A1048 "
        pdb=" CG  MET A1048 "
      ideal   model   delta    sigma   weight residual
     114.10  121.09   -6.99 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" N   GLY A 380 "
        pdb=" CA  GLY A 380 "
        pdb=" C   GLY A 380 "
      ideal   model   delta    sigma   weight residual
     115.08  111.46    3.62 1.19e+00 7.06e-01 9.27e+00
  angle pdb=" N   ALA A 854 "
        pdb=" CA  ALA A 854 "
        pdb=" C   ALA A 854 "
      ideal   model   delta    sigma   weight residual
     114.04  110.47    3.57 1.24e+00 6.50e-01 8.27e+00
  ... (remaining 9657 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 3971
       17.69 -    35.38: 379
       35.38 -    53.07: 67
       53.07 -    70.76: 12
       70.76 -    88.44: 5
  Dihedral angle restraints: 4434
    sinusoidal: 1848
      harmonic: 2586
  Sorted by residual:
  dihedral pdb=" CB  CYS A 559 "
           pdb=" SG  CYS A 559 "
           pdb=" SG  CYS A 566 "
           pdb=" CB  CYS A 566 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -164.96   78.96     1      1.00e+01 1.00e-02 7.76e+01
  dihedral pdb=" CA  GLN A1052 "
           pdb=" C   GLN A1052 "
           pdb=" N   ILE A1053 "
           pdb=" CA  ILE A1053 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.57  -19.43     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  GLU A 402 "
           pdb=" C   GLU A 402 "
           pdb=" N   TRP A 403 "
           pdb=" CA  TRP A 403 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.16  -17.84     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 4431 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 851
       0.045 -    0.089: 176
       0.089 -    0.134: 49
       0.134 -    0.178: 1
       0.178 -    0.223: 3
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CA  PHE A 551 "
            pdb=" N   PHE A 551 "
            pdb=" C   PHE A 551 "
            pdb=" CB  PHE A 551 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL A1139 "
            pdb=" CA  VAL A1139 "
            pdb=" CG1 VAL A1139 "
            pdb=" CG2 VAL A1139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.74e-01
  chirality pdb=" CA  PRO A 597 "
            pdb=" N   PRO A 597 "
            pdb=" C   PRO A 597 "
            pdb=" CB  PRO A 597 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 8.38e-01
  ... (remaining 1077 not shown)

  Planarity restraints: 1268
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 553 "   -0.036 5.00e-02 4.00e+02   5.49e-02 4.82e+00
        pdb=" N   PRO A 554 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 554 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 554 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 908 "    0.010 2.00e-02 2.50e+03   1.30e-02 3.38e+00
        pdb=" CG  TYR A 908 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 908 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 908 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 908 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 908 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 908 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 908 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 475 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.52e+00
        pdb=" N   PRO A 476 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 476 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 476 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1265 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1395
        2.77 -     3.30: 7028
        3.30 -     3.84: 11168
        3.84 -     4.37: 12436
        4.37 -     4.90: 21066
  Nonbonded interactions: 53093
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 867 "
            pdb=" NZ  LYS A 896 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OG  SER A 808 "
            pdb=" O   LEU A 870 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG  SER A 228 "
            pdb=" OD1 ASP A 230 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" NZ  LYS A 747 "
            pdb=" OD2 ASP A 751 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" OD1 ASP A 685 "
            pdb=" ND2 ASN A 689 "
     model   vdw
     2.278 3.120
  ... (remaining 53088 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:             1.540
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.960
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
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      :  0.003   0.074   7152  Z= 0.161
  Angle     :  0.648  11.739   9664  Z= 0.368
  Chirality :  0.040   0.223   1080
  Planarity :  0.004   0.055   1268
  Dihedral  : 14.130  88.444   2753
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.61 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.29), residues: 881
  helix:  2.00 (0.24), residues: 479
  sheet: -0.19 (0.70), residues: 44
  loop : -0.13 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 403 
 HIS   0.004   0.001   HIS A 248 
 PHE   0.023   0.001   PHE A 551 
 TYR   0.032   0.001   TYR A 908 
 ARG   0.006   0.000   ARG A 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14478 (  384)
  hydrogen bonds       : angle       4.85871 ( 1104)
  SS BOND              : bond        0.00392 (    1)
  SS BOND              : angle       1.52198 (    2)
  covalent geometry    : bond        0.00316 ( 7151)
  covalent geometry    : angle       0.64743 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  823 LYS cc_start: 0.8869 (mttt) cc_final: 0.8663 (tptm)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.2458
  time to fit residues: 21.6122
Evaluate side-chains
  53 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 672 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.129397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.088824 restraints weight = 15098.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.092314 restraints weight = 9029.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.094654 restraints weight = 6578.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7152  Z= 0.139
  Angle     :  0.552   7.566   9664  Z= 0.288
  Chirality :  0.040   0.198   1080
  Planarity :  0.004   0.047   1268
  Dihedral  :  4.495  18.355    944
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  8.44 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.29), residues: 881
  helix:  1.97 (0.23), residues: 489
  sheet: -0.42 (0.67), residues: 45
  loop :  0.03 (0.36), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 714 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.020   0.001   PHE A 551 
 TYR   0.024   0.001   TYR A 550 
 ARG   0.004   0.000   ARG A 664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04811 (  384)
  hydrogen bonds       : angle       4.16504 ( 1104)
  SS BOND              : bond        0.00242 (    1)
  SS BOND              : angle       1.45681 (    2)
  covalent geometry    : bond        0.00314 ( 7151)
  covalent geometry    : angle       0.55194 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  701 MET cc_start: 0.7654 (mmm) cc_final: 0.7427 (mmm)
REVERT: A  740 LEU cc_start: 0.8748 (tp) cc_final: 0.8533 (tp)
REVERT: A  823 LYS cc_start: 0.8872 (mttt) cc_final: 0.8659 (tptm)
  outliers start: 9
  outliers final: 4
  residues processed: 69
  average time/residue: 0.1959
  time to fit residues: 18.5731
Evaluate side-chains
  55 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  849 VAL
Chi-restraints excluded: chain A residue  862 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 81 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 587 GLN
A 672 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.129287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.088515 restraints weight = 15285.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.091978 restraints weight = 9142.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.094345 restraints weight = 6640.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7152  Z= 0.133
  Angle     :  0.545   7.419   9664  Z= 0.280
  Chirality :  0.039   0.153   1080
  Planarity :  0.004   0.047   1268
  Dihedral  :  4.335  16.712    944
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.26 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.29), residues: 881
  helix:  2.08 (0.23), residues: 489
  sheet: -0.53 (0.68), residues: 45
  loop :  0.10 (0.36), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 714 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.020   0.001   PHE A 551 
 TYR   0.016   0.001   TYR A 256 
 ARG   0.004   0.000   ARG A 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04607 (  384)
  hydrogen bonds       : angle       4.02337 ( 1104)
  SS BOND              : bond        0.00278 (    1)
  SS BOND              : angle       1.46523 (    2)
  covalent geometry    : bond        0.00305 ( 7151)
  covalent geometry    : angle       0.54424 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  701 MET cc_start: 0.7762 (mmm) cc_final: 0.7546 (mmm)
REVERT: A  740 LEU cc_start: 0.8885 (tp) cc_final: 0.8663 (tp)
REVERT: A  823 LYS cc_start: 0.8895 (mttt) cc_final: 0.8663 (tptm)
REVERT: A  908 TYR cc_start: 0.6476 (p90) cc_final: 0.6222 (p90)
  outliers start: 12
  outliers final: 7
  residues processed: 71
  average time/residue: 0.2012
  time to fit residues: 19.7566
Evaluate side-chains
  59 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  819 THR
Chi-restraints excluded: chain A residue  849 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 672 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.138093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.103488 restraints weight = 15453.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.107117 restraints weight = 10460.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.108643 restraints weight = 6690.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7152  Z= 0.132
  Angle     :  0.530   8.031   9664  Z= 0.272
  Chirality :  0.039   0.181   1080
  Planarity :  0.004   0.048   1268
  Dihedral  :  4.201  16.657    944
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.04 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.29), residues: 881
  helix:  2.18 (0.23), residues: 488
  sheet: -0.54 (0.69), residues: 45
  loop :  0.11 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 403 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.020   0.001   PHE A 551 
 TYR   0.026   0.001   TYR A 550 
 ARG   0.004   0.000   ARG A 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04384 (  384)
  hydrogen bonds       : angle       3.96943 ( 1104)
  SS BOND              : bond        0.00271 (    1)
  SS BOND              : angle       1.40776 (    2)
  covalent geometry    : bond        0.00305 ( 7151)
  covalent geometry    : angle       0.53013 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 LEU cc_start: 0.9041 (tp) cc_final: 0.8832 (tp)
REVERT: A  908 TYR cc_start: 0.6494 (p90) cc_final: 0.6253 (p90)
  outliers start: 13
  outliers final: 11
  residues processed: 72
  average time/residue: 0.1919
  time to fit residues: 19.2442
Evaluate side-chains
  64 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  725 ASN
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  819 THR
Chi-restraints excluded: chain A residue  849 VAL
Chi-restraints excluded: chain A residue 1069 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0770
   chunk 46 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A 672 HIS
A 703 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.138514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.103657 restraints weight = 15214.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.106255 restraints weight = 10340.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.108196 restraints weight = 6643.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7152  Z= 0.120
  Angle     :  0.524   8.010   9664  Z= 0.264
  Chirality :  0.039   0.227   1080
  Planarity :  0.004   0.050   1268
  Dihedral  :  4.103  16.445    944
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 11.30 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.29), residues: 881
  helix:  2.26 (0.23), residues: 488
  sheet: -0.45 (0.71), residues: 45
  loop :  0.14 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 687 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.019   0.001   PHE A 551 
 TYR   0.011   0.001   TYR A 256 
 ARG   0.003   0.000   ARG A1180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04135 (  384)
  hydrogen bonds       : angle       3.91986 ( 1104)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       1.33209 (    2)
  covalent geometry    : bond        0.00274 ( 7151)
  covalent geometry    : angle       0.52322 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.7793 (tp30) cc_final: 0.7553 (tm-30)
REVERT: A  882 ASP cc_start: 0.7282 (m-30) cc_final: 0.7000 (p0)
REVERT: A  908 TYR cc_start: 0.6516 (p90) cc_final: 0.6311 (p90)
  outliers start: 12
  outliers final: 11
  residues processed: 68
  average time/residue: 0.1930
  time to fit residues: 18.4343
Evaluate side-chains
  62 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  725 ASN
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  819 THR
Chi-restraints excluded: chain A residue  849 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 672 HIS
A 703 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.134675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.095844 restraints weight = 15464.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.099352 restraints weight = 9313.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.101647 restraints weight = 6788.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7152  Z= 0.207
  Angle     :  0.602   7.625   9664  Z= 0.306
  Chirality :  0.042   0.162   1080
  Planarity :  0.004   0.049   1268
  Dihedral  :  4.356  16.620    944
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 11.17 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.29), residues: 881
  helix:  2.11 (0.23), residues: 489
  sheet: -0.61 (0.71), residues: 45
  loop :  0.14 (0.36), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 687 
 HIS   0.005   0.001   HIS A 248 
 PHE   0.021   0.002   PHE A 551 
 TYR   0.025   0.002   TYR A 550 
 ARG   0.003   0.000   ARG A1180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05236 (  384)
  hydrogen bonds       : angle       4.14249 ( 1104)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       1.76054 (    2)
  covalent geometry    : bond        0.00485 ( 7151)
  covalent geometry    : angle       0.60195 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 50
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.8018 (tp30) cc_final: 0.7593 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 66
  average time/residue: 0.1691
  time to fit residues: 16.1981
Evaluate side-chains
  61 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  725 ASN
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  819 THR
Chi-restraints excluded: chain A residue  849 VAL
Chi-restraints excluded: chain A residue 1069 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 8 optimal weight:    0.1980
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 672 HIS
A 703 HIS
** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.136774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.098099 restraints weight = 15317.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.101687 restraints weight = 9139.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.104052 restraints weight = 6641.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7152  Z= 0.120
  Angle     :  0.530  10.654   9664  Z= 0.269
  Chirality :  0.039   0.143   1080
  Planarity :  0.004   0.052   1268
  Dihedral  :  4.128  16.272    944
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.51 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.29), residues: 881
  helix:  2.29 (0.23), residues: 488
  sheet: -0.51 (0.72), residues: 45
  loop :  0.16 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 403 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.020   0.001   PHE A 551 
 TYR   0.026   0.001   TYR A 550 
 ARG   0.003   0.000   ARG A1180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04193 (  384)
  hydrogen bonds       : angle       3.89737 ( 1104)
  SS BOND              : bond        0.00276 (    1)
  SS BOND              : angle       1.53022 (    2)
  covalent geometry    : bond        0.00274 ( 7151)
  covalent geometry    : angle       0.52974 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.7926 (tp30) cc_final: 0.7505 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 59
  average time/residue: 0.1757
  time to fit residues: 15.0498
Evaluate side-chains
  53 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  849 VAL
Chi-restraints excluded: chain A residue 1064 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 4 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0970
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 703 HIS
** A1050 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 = 0.4063 r_free = 0.4063 target = 0.137020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.098221 restraints weight = 15470.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.101772 restraints weight = 9231.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.104220 restraints weight = 6715.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7152  Z= 0.122
  Angle     :  0.534   9.770   9664  Z= 0.268
  Chirality :  0.039   0.140   1080
  Planarity :  0.004   0.051   1268
  Dihedral  :  4.078  16.126    944
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.38 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.29), residues: 881
  helix:  2.29 (0.24), residues: 491
  sheet: -0.43 (0.72), residues: 45
  loop :  0.18 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 403 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.019   0.001   PHE A 551 
 TYR   0.026   0.001   TYR A 550 
 ARG   0.002   0.000   ARG A1180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04115 (  384)
  hydrogen bonds       : angle       3.91378 ( 1104)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       1.36939 (    2)
  covalent geometry    : bond        0.00279 ( 7151)
  covalent geometry    : angle       0.53335 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.7968 (tp30) cc_final: 0.7557 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 58
  average time/residue: 0.1903
  time to fit residues: 15.5282
Evaluate side-chains
  53 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  819 THR
Chi-restraints excluded: chain A residue  849 VAL
Chi-restraints excluded: chain A residue 1064 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 23 optimal weight:    0.4980
   chunk 66 optimal weight:    0.7980
   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 703 HIS
** A1050 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 = 0.4060 r_free = 0.4060 target = 0.136717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.097761 restraints weight = 15498.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.101393 restraints weight = 9240.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.103794 restraints weight = 6677.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7152  Z= 0.129
  Angle     :  0.554   9.254   9664  Z= 0.276
  Chirality :  0.039   0.148   1080
  Planarity :  0.004   0.051   1268
  Dihedral  :  4.063  16.219    944
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.38 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.29), residues: 881
  helix:  2.28 (0.24), residues: 490
  sheet: -0.47 (0.73), residues: 45
  loop :  0.19 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 403 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.019   0.001   PHE A 551 
 TYR   0.026   0.001   TYR A 550 
 ARG   0.005   0.000   ARG A 664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04113 (  384)
  hydrogen bonds       : angle       3.89791 ( 1104)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       1.35877 (    2)
  covalent geometry    : bond        0.00300 ( 7151)
  covalent geometry    : angle       0.55414 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.8031 (tp30) cc_final: 0.7624 (tm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 57
  average time/residue: 0.2061
  time to fit residues: 16.4627
Evaluate side-chains
  54 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  819 THR
Chi-restraints excluded: chain A residue  849 VAL
Chi-restraints excluded: chain A residue 1064 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0670
   chunk 74 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
A 703 HIS
** A1050 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 = 0.4091 r_free = 0.4091 target = 0.137984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.099691 restraints weight = 15730.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.103292 restraints weight = 9260.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.105738 restraints weight = 6673.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7152  Z= 0.128
  Angle     :  0.550  10.854   9664  Z= 0.274
  Chirality :  0.039   0.143   1080
  Planarity :  0.004   0.051   1268
  Dihedral  :  4.020  16.135    944
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 13.51 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.29), residues: 881
  helix:  2.30 (0.24), residues: 490
  sheet: -0.50 (0.72), residues: 45
  loop :  0.19 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 403 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.019   0.001   PHE A 551 
 TYR   0.027   0.001   TYR A 550 
 ARG   0.002   0.000   ARG A1180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04072 (  384)
  hydrogen bonds       : angle       3.89172 ( 1104)
  SS BOND              : bond        0.00265 (    1)
  SS BOND              : angle       1.35350 (    2)
  covalent geometry    : bond        0.00295 ( 7151)
  covalent geometry    : angle       0.54993 ( 9662)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.8019 (tp30) cc_final: 0.7603 (tm-30)
REVERT: A 1181 MET cc_start: 0.8248 (tpp) cc_final: 0.8026 (tpt)
  outliers start: 8
  outliers final: 8
  residues processed: 57
  average time/residue: 0.2021
  time to fit residues: 16.2757
Evaluate side-chains
  54 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  819 THR
Chi-restraints excluded: chain A residue  849 VAL
Chi-restraints excluded: chain A residue 1064 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 78 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 60 optimal weight:    0.2980
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   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 703 HIS
** A1050 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 = 0.4096 r_free = 0.4096 target = 0.138392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.100204 restraints weight = 15390.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.103813 restraints weight = 9077.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.106218 restraints weight = 6557.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7152  Z= 0.124
  Angle     :  0.556  10.354   9664  Z= 0.277
  Chirality :  0.039   0.140   1080
  Planarity :  0.004   0.052   1268
  Dihedral  :  3.969  16.182    944
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.25 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.02 (0.29), residues: 881
  helix:  2.31 (0.24), residues: 491
  sheet: -0.47 (0.73), residues: 45
  loop :  0.23 (0.36), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 403 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.019   0.001   PHE A 551 
 TYR   0.027   0.001   TYR A 550 
 ARG   0.007   0.000   ARG A 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04003 (  384)
  hydrogen bonds       : angle       3.86544 ( 1104)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       1.32524 (    2)
  covalent geometry    : bond        0.00290 ( 7151)
  covalent geometry    : angle       0.55573 ( 9662)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2569.10 seconds
wall clock time: 45 minutes 19.83 seconds (2719.83 seconds total)