Starting phenix.real_space_refine
on Sat Oct 11 11:15:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qee_18353/10_2025/8qee_18353_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qee_18353/10_2025/8qee_18353.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qee_18353/10_2025/8qee_18353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qee_18353/10_2025/8qee_18353.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qee_18353/10_2025/8qee_18353_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qee_18353/10_2025/8qee_18353_trim.cif"
  }
  resolution = 2.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.066
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: 5
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    4411      2.51       5
     N    1054      2.21       5
     O    1359      1.98       5
     H    6889      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13746
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 13251
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 823, 13251
          Classifications: {'peptide': 823}
          Link IDs: {'PTRANS': 34, 'TRANS': 788}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 467
          Unusual residues: {'NAG': 3, 'Y01': 1}
          Classifications: {'undetermined': 4, 'water': 130}
          Link IDs: {None: 133}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 2.75, per 1000 atoms: 0.20
  Number of scatterers: 13746
  At special positions: 0
  Unit cell: (74.405, 76.993, 137.811, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     O    1359      8.00
     N    1054      7.00
     C    4411      6.00
     H    6889      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 438 " - pdb=" SG  CYS A 447 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 473 " - pdb=" SG  CYS A 480 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 822 " - pdb=" SG  CYS A 828 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 868 " - pdb=" SG  CYS A 925 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 869 " - pdb=" SG  CYS A 891 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 879 " - pdb=" SG  CYS A 888 " 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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A1202 " - " ASN A 401 "
      " NAG A1203 " - " ASN A 940 "
      " NAG A1204 " - " ASN A 900 "
      " NAG B   1 " - " ASN A 513 "
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 392.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 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:
      41 helices and 3 sheets defined
      67.9% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 324 through 337
      removed outlier: 4.193A  pdb=" N   THR A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 360
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 375 through 389
    Processing helix  chain 'A' and resid 408 through 425
    Processing helix  chain 'A' and resid 451 through 457
    Processing helix  chain 'A' and resid 465 through 476
    Processing helix  chain 'A' and resid 477 through 481
    Processing helix  chain 'A' and resid 489 through 494
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 515 through 531
      removed outlier: 3.662A  pdb=" N   ASN A 519 " --> pdb=" O   THR A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 553
    Processing helix  chain 'A' and resid 557 through 576
    Processing helix  chain 'A' and resid 584 through 609
      removed outlier: 3.731A  pdb=" N   LEU A 608 " --> pdb=" O   GLY A 604 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 620
    Processing helix  chain 'A' and resid 620 through 630
      removed outlier: 3.895A  pdb=" N   ILE A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 646
      removed outlier: 3.624A  pdb=" N   PHE A 634 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLU A 645 " --> pdb=" O   ASP A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 682
      Proline residue:  A 665  - end of helix
    Processing helix  chain 'A' and resid 686 through 722
      removed outlier: 3.764A  pdb=" N   TYR A 711 " --> pdb=" O   GLN A 707 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   VAL A 712 " --> pdb=" O   LEU A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 745
      removed outlier: 3.935A  pdb=" N   TYR A 742 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE A 743 " --> pdb=" O   LYS A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 767
      removed outlier: 3.574A  pdb=" N   PHE A 766 " --> pdb=" O   THR A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 770
      No H-bonds generated for 'chain 'A' and resid 768 through 770'
    Processing helix  chain 'A' and resid 775 through 780
      removed outlier: 3.630A  pdb=" N   ALA A 779 " --> pdb=" O   ASP A 775 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL A 780 " --> pdb=" O   GLN A 776 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 775 through 780'
    Processing helix  chain 'A' and resid 784 through 797
      removed outlier: 4.357A  pdb=" N   ASP A 788 " --> pdb=" O   SER A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 820
    Processing helix  chain 'A' and resid 832 through 841
    Processing helix  chain 'A' and resid 852 through 861
    Processing helix  chain 'A' and resid 907 through 918
      removed outlier: 3.721A  pdb=" N   MET A 911 " --> pdb=" O   GLY A 907 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ILE A 916 " --> pdb=" O   GLU A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 934
    Processing helix  chain 'A' and resid 958 through 974
    Processing helix  chain 'A' and resid 987 through 995
      removed outlier: 4.002A  pdb=" N   VAL A 992 " --> pdb=" O   ILE A 989 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   GLN A 993 " --> pdb=" O   PHE A 990 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TYR A 994 " --> pdb=" O   PHE A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1021
    Processing helix  chain 'A' and resid 1022 through 1048
    Processing helix  chain 'A' and resid 1052 through 1079
      removed outlier: 3.505A  pdb=" N   GLY A1064 " --> pdb=" O   ILE A1060 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   HIS A1072 " --> pdb=" O   GLU A1068 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   ILE A1073 " --> pdb=" O   PHE A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1087 through 1097
    Processing helix  chain 'A' and resid 1099 through 1107
    Processing helix  chain 'A' and resid 1107 through 1117
      removed outlier: 4.708A  pdb=" N   VAL A1117 " --> pdb=" O   ILE A1113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1121
    Processing helix  chain 'A' and resid 1124 through 1129
    Processing helix  chain 'A' and resid 1130 through 1147
    Processing helix  chain 'A' and resid 1147 through 1155
    Processing sheet with id=AA1, first strand: chain 'A' and resid 449 through 450
    Processing sheet with id=AA2, first strand: chain 'A' and resid 937 through 939
      removed outlier: 4.311A  pdb=" N   ASP A 980 " --> pdb=" O   LYS A 808 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 870 through 872

    405 hydrogen bonds defined for protein.
    1173 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: 3.21

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6882
        1.03 -     1.23: 63
        1.23 -     1.43: 2859
        1.43 -     1.62: 3933
        1.62 -     1.82: 47
  Bond restraints: 13784
  Sorted by residual:
  bond pdb=" C1  NAG A1202 "
       pdb=" O5  NAG A1202 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.15e+00
  bond pdb=" N   ALA A 324 "
       pdb=" CA  ALA A 324 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  bond pdb=" N   ALA A 324 "
       pdb=" H   ALA A 324 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.31e+00
  bond pdb=" C1  NAG A1204 "
       pdb=" O5  NAG A1204 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" C1  NAG A1203 "
       pdb=" O5  NAG A1203 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.58e+00
  ... (remaining 13779 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.92: 22175
        0.92 -     1.84: 2088
        1.84 -     2.76: 98
        2.76 -     3.68: 163
        3.68 -     4.60: 12
  Bond angle restraints: 24536
  Sorted by residual:
  angle pdb=" N   SER A 429 "
        pdb=" CA  SER A 429 "
        pdb=" C   SER A 429 "
      ideal   model   delta    sigma   weight residual
     110.80  106.47    4.33 2.13e+00 2.20e-01 4.14e+00
  angle pdb=" N   GLU A 430 "
        pdb=" CA  GLU A 430 "
        pdb=" C   GLU A 430 "
      ideal   model   delta    sigma   weight residual
     113.72  110.91    2.81 1.52e+00 4.33e-01 3.42e+00
  angle pdb=" CB  GLN A 893 "
        pdb=" CG  GLN A 893 "
        pdb=" CD  GLN A 893 "
      ideal   model   delta    sigma   weight residual
     112.60  115.37   -2.77 1.70e+00 3.46e-01 2.65e+00
  angle pdb=" C5  NAG B   1 "
        pdb=" C4  NAG B   1 "
        pdb=" O4  NAG B   1 "
      ideal   model   delta    sigma   weight residual
     111.70  107.10    4.60 3.00e+00 1.11e-01 2.35e+00
  angle pdb=" CA  ALA A 324 "
        pdb=" N   ALA A 324 "
        pdb=" H   ALA A 324 "
      ideal   model   delta    sigma   weight residual
     114.00  109.46    4.54 3.00e+00 1.11e-01 2.29e+00
  ... (remaining 24531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.81: 6084
       23.81 -    47.62: 337
       47.62 -    71.42: 102
       71.42 -    95.23: 17
       95.23 -   119.04: 3
  Dihedral angle restraints: 6543
    sinusoidal: 3545
      harmonic: 2998
  Sorted by residual:
  dihedral pdb=" CA  SER A 428 "
           pdb=" C   SER A 428 "
           pdb=" N   SER A 429 "
           pdb=" CA  SER A 429 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.43  -21.57     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CB  CYS A 822 "
           pdb=" SG  CYS A 822 "
           pdb=" SG  CYS A 828 "
           pdb=" CB  CYS A 828 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -120.43   34.43     1      1.00e+01 1.00e-02 1.68e+01
  dihedral pdb=" CA  SER A 429 "
           pdb=" C   SER A 429 "
           pdb=" N   GLU A 430 "
           pdb=" CA  GLU A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.64  -20.36     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 6540 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1010
       0.071 -    0.141: 84
       0.141 -    0.212: 0
       0.212 -    0.282: 0
       0.282 -    0.353: 1
  Chirality restraints: 1095
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 513 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CA  VAL A 944 "
            pdb=" N   VAL A 944 "
            pdb=" C   VAL A 944 "
            pdb=" CB  VAL A 944 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.01e-01
  chirality pdb=" CA  ILE A 449 "
            pdb=" N   ILE A 449 "
            pdb=" C   ILE A 449 "
            pdb=" CB  ILE A 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 1092 not shown)

  Planarity restraints: 1954
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 931 "   -0.022 5.00e-02 4.00e+02   3.27e-02 1.72e+00
        pdb=" N   PRO A 932 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 932 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 932 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 985 "    0.018 5.00e-02 4.00e+02   2.77e-02 1.23e+00
        pdb=" N   PRO A 986 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 986 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 986 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 998 "    0.017 5.00e-02 4.00e+02   2.64e-02 1.11e+00
        pdb=" N   PRO A 999 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 999 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 999 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1951 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 1682
        2.24 -     2.83: 31066
        2.83 -     3.42: 39699
        3.42 -     4.01: 56055
        4.01 -     4.60: 83492
  Nonbonded interactions: 211994
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 653 "
            pdb=" HZ1 LYS A 720 "
     model   vdw
     1.652 2.450
  nonbonded pdb=" O   SER A 428 "
            pdb=" HG  SER A 429 "
     model   vdw
     1.652 2.450
  nonbonded pdb=" O   ILE A 633 "
            pdb=" HG1 THR A 637 "
     model   vdw
     1.655 2.450
  nonbonded pdb=" HH  TYR A 455 "
            pdb=" O   LEU A 488 "
     model   vdw
     1.663 2.450
  nonbonded pdb=" O   ALA A 758 "
            pdb=" HG1 THR A 762 "
     model   vdw
     1.668 2.450
  ... (remaining 211989 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.360
  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:             0.090
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     14.220
  Find NCS groups from input model:        0.040
  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:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
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      :  0.002   0.041   6906  Z= 0.108
  Angle     :  0.462   6.303   9403  Z= 0.227
  Chirality :  0.038   0.353   1095
  Planarity :  0.003   0.033   1163
  Dihedral  : 17.851 119.040   2609
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.05 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.31), residues: 819
  helix:  1.73 (0.24), residues: 486
  sheet:  2.21 (0.89), residues: 42
  loop :  1.53 (0.42), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1075 
 TYR   0.007   0.001   TYR A 984 
 PHE   0.008   0.001   PHE A 505 
 TRP   0.007   0.001   TRP A 897 
 HIS   0.004   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6895)
  covalent geometry    : angle       0.44747 ( 9376)
  SS BOND              : bond        0.00120 (    6)
  SS BOND              : angle       0.38470 (   12)
  hydrogen bonds       : bond        0.21133 (  405)
  hydrogen bonds       : angle       7.46558 ( 1173)
  link_BETA1-4         : bond        0.00118 (    1)
  link_BETA1-4         : angle       3.21860 (    3)
  link_NAG-ASN         : bond        0.00448 (    4)
  link_NAG-ASN         : angle       2.87730 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A  662 ARG cc_start: 0.7502 (ptp90) cc_final: 0.6713 (ptm160)
  outliers start: 16
  outliers final: 14
  residues processed: 98
  average time/residue: 0.9828
  time to fit residues: 102.8017
Evaluate side-chains
  97 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  943 SER
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1099 ILE
Chi-restraints excluded: chain A residue 1125 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 420 ASN
A 954 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.148810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.125451 restraints weight = 20694.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.47
r_work: 0.3348 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.0801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6906  Z= 0.168
  Angle     :  0.569   7.228   9403  Z= 0.305
  Chirality :  0.041   0.179   1095
  Planarity :  0.004   0.035   1163
  Dihedral  :  9.338  87.649   1078
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.97 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.30), residues: 819
  helix:  1.59 (0.23), residues: 495
  sheet:  1.85 (0.80), residues: 43
  loop :  1.49 (0.42), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 662 
 TYR   0.015   0.001   TYR A 711 
 PHE   0.019   0.002   PHE A 505 
 TRP   0.011   0.002   TRP A 415 
 HIS   0.004   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6895)
  covalent geometry    : angle       0.55889 ( 9376)
  SS BOND              : bond        0.00147 (    6)
  SS BOND              : angle       0.46781 (   12)
  hydrogen bonds       : bond        0.06321 (  405)
  hydrogen bonds       : angle       5.57071 ( 1173)
  link_BETA1-4         : bond        0.00476 (    1)
  link_BETA1-4         : angle       1.93170 (    3)
  link_NAG-ASN         : bond        0.00416 (    4)
  link_NAG-ASN         : angle       2.83799 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1068 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7088 (tt0)
  outliers start: 19
  outliers final: 11
  residues processed: 100
  average time/residue: 0.9997
  time to fit residues: 106.8810
Evaluate side-chains
  92 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  658 SER
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  943 SER
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1068 GLU
Chi-restraints excluded: chain A residue 1125 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 691 ASN
A 865 ASN
A 954 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.146863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123237 restraints weight = 20610.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.46
r_work: 0.3317 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6906  Z= 0.221
  Angle     :  0.616   8.162   9403  Z= 0.324
  Chirality :  0.043   0.167   1095
  Planarity :  0.004   0.039   1163
  Dihedral  :  7.541  59.745   1069
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.84 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.30), residues: 819
  helix:  1.14 (0.22), residues: 495
  sheet:  1.45 (0.76), residues: 43
  loop :  1.21 (0.42), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 393 
 TYR   0.015   0.002   TYR A 711 
 PHE   0.023   0.002   PHE A 505 
 TRP   0.012   0.002   TRP A 415 
 HIS   0.003   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 6895)
  covalent geometry    : angle       0.60095 ( 9376)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       0.58518 (   12)
  hydrogen bonds       : bond        0.05984 (  405)
  hydrogen bonds       : angle       5.30156 ( 1173)
  link_BETA1-4         : bond        0.00068 (    1)
  link_BETA1-4         : angle       2.26432 (    3)
  link_NAG-ASN         : bond        0.00576 (    4)
  link_NAG-ASN         : angle       3.66047 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7416 (mp)
REVERT: A 1068 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7122 (tt0)
REVERT: A 1075 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7282 (ttt90)
  outliers start: 19
  outliers final: 11
  residues processed: 100
  average time/residue: 1.0686
  time to fit residues: 113.7565
Evaluate side-chains
  97 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  658 SER
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1068 GLU
Chi-restraints excluded: chain A residue 1075 ARG
Chi-restraints excluded: chain A residue 1125 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 66 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 954 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.149169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.125641 restraints weight = 20563.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.46
r_work: 0.3351 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6906  Z= 0.141
  Angle     :  0.539   6.277   9403  Z= 0.285
  Chirality :  0.040   0.183   1095
  Planarity :  0.004   0.039   1163
  Dihedral  :  6.900  59.607   1067
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.64 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.30), residues: 819
  helix:  1.27 (0.23), residues: 497
  sheet:  1.40 (0.75), residues: 43
  loop :  1.33 (0.42), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 393 
 TYR   0.014   0.001   TYR A 711 
 PHE   0.019   0.001   PHE A 505 
 TRP   0.012   0.001   TRP A 415 
 HIS   0.005   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6895)
  covalent geometry    : angle       0.52867 ( 9376)
  SS BOND              : bond        0.00136 (    6)
  SS BOND              : angle       0.44267 (   12)
  hydrogen bonds       : bond        0.04947 (  405)
  hydrogen bonds       : angle       5.11513 ( 1173)
  link_BETA1-4         : bond        0.00045 (    1)
  link_BETA1-4         : angle       2.16967 (    3)
  link_NAG-ASN         : bond        0.00471 (    4)
  link_NAG-ASN         : angle       2.83033 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7001 (t80) cc_final: 0.6540 (t80)
REVERT: A  412 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7445 (mp)
REVERT: A 1019 PHE cc_start: 0.8150 (m-80) cc_final: 0.7905 (m-80)
REVERT: A 1068 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7014 (tp30)
REVERT: A 1075 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7216 (ttt90)
  outliers start: 17
  outliers final: 9
  residues processed: 101
  average time/residue: 1.1252
  time to fit residues: 120.7955
Evaluate side-chains
  99 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  658 SER
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  842 HIS
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1068 GLU
Chi-restraints excluded: chain A residue 1075 ARG
Chi-restraints excluded: chain A residue 1125 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 48 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 54 optimal weight:    6.9990
   chunk 50 optimal weight:    0.6980
   chunk 1 optimal weight:    0.1980
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 691 ASN
A 954 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.150195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.126661 restraints weight = 20593.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.47
r_work: 0.3364 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6906  Z= 0.124
  Angle     :  0.516   5.985   9403  Z= 0.274
  Chirality :  0.039   0.189   1095
  Planarity :  0.004   0.038   1163
  Dihedral  :  6.594  59.606   1065
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.78 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.30), residues: 819
  helix:  1.36 (0.23), residues: 499
  sheet:  1.46 (0.75), residues: 43
  loop :  1.37 (0.43), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 393 
 TYR   0.013   0.001   TYR A 711 
 PHE   0.018   0.001   PHE A 505 
 TRP   0.012   0.001   TRP A 415 
 HIS   0.004   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6895)
  covalent geometry    : angle       0.50653 ( 9376)
  SS BOND              : bond        0.00116 (    6)
  SS BOND              : angle       0.37203 (   12)
  hydrogen bonds       : bond        0.04641 (  405)
  hydrogen bonds       : angle       4.99738 ( 1173)
  link_BETA1-4         : bond        0.00038 (    1)
  link_BETA1-4         : angle       2.15278 (    3)
  link_NAG-ASN         : bond        0.00498 (    4)
  link_NAG-ASN         : angle       2.66823 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.6944 (t80) cc_final: 0.6565 (t80)
REVERT: A  412 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7456 (mp)
REVERT: A  662 ARG cc_start: 0.7614 (ptp90) cc_final: 0.7370 (tmm-80)
REVERT: A 1019 PHE cc_start: 0.8126 (m-80) cc_final: 0.7896 (m-80)
REVERT: A 1068 GLU cc_start: 0.7373 (tt0) cc_final: 0.6924 (tp30)
REVERT: A 1075 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7226 (ttt90)
  outliers start: 15
  outliers final: 9
  residues processed: 100
  average time/residue: 1.1464
  time to fit residues: 122.0326
Evaluate side-chains
  100 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  658 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  842 HIS
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1075 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 954 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.148376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.124748 restraints weight = 20467.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.45
r_work: 0.3339 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6906  Z= 0.179
  Angle     :  0.559   7.364   9403  Z= 0.295
  Chirality :  0.040   0.175   1095
  Planarity :  0.004   0.037   1163
  Dihedral  :  6.674  59.179   1062
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.71 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.64 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.30), residues: 819
  helix:  1.23 (0.23), residues: 499
  sheet:  1.38 (0.75), residues: 43
  loop :  1.27 (0.42), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 393 
 TYR   0.014   0.002   TYR A 711 
 PHE   0.021   0.002   PHE A 505 
 TRP   0.012   0.002   TRP A 415 
 HIS   0.003   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 6895)
  covalent geometry    : angle       0.54594 ( 9376)
  SS BOND              : bond        0.00155 (    6)
  SS BOND              : angle       0.48326 (   12)
  hydrogen bonds       : bond        0.05085 (  405)
  hydrogen bonds       : angle       5.04932 ( 1173)
  link_BETA1-4         : bond        0.00021 (    1)
  link_BETA1-4         : angle       2.26849 (    3)
  link_NAG-ASN         : bond        0.00511 (    4)
  link_NAG-ASN         : angle       3.22132 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.6986 (t80) cc_final: 0.6561 (t80)
REVERT: A  412 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7522 (mp)
REVERT: A  662 ARG cc_start: 0.7581 (ptp90) cc_final: 0.7305 (tmm-80)
REVERT: A 1019 PHE cc_start: 0.8152 (m-80) cc_final: 0.7923 (m-80)
REVERT: A 1068 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6992 (tp30)
REVERT: A 1075 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7278 (ttt90)
  outliers start: 17
  outliers final: 11
  residues processed: 103
  average time/residue: 1.1060
  time to fit residues: 121.2933
Evaluate side-chains
  103 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  658 SER
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  842 HIS
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1068 GLU
Chi-restraints excluded: chain A residue 1075 ARG
Chi-restraints excluded: chain A residue 1125 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 954 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.147887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.124185 restraints weight = 20464.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.46
r_work: 0.3334 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6906  Z= 0.187
  Angle     :  0.573   7.658   9403  Z= 0.303
  Chirality :  0.041   0.181   1095
  Planarity :  0.004   0.039   1163
  Dihedral  :  6.719  58.691   1062
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.83 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.78 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.30), residues: 819
  helix:  1.19 (0.23), residues: 497
  sheet:  1.36 (0.75), residues: 43
  loop :  1.19 (0.42), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 393 
 TYR   0.015   0.002   TYR A 711 
 PHE   0.022   0.002   PHE A 505 
 TRP   0.012   0.002   TRP A 415 
 HIS   0.003   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 6895)
  covalent geometry    : angle       0.55931 ( 9376)
  SS BOND              : bond        0.00164 (    6)
  SS BOND              : angle       0.51756 (   12)
  hydrogen bonds       : bond        0.05151 (  405)
  hydrogen bonds       : angle       5.07341 ( 1173)
  link_BETA1-4         : bond        0.00013 (    1)
  link_BETA1-4         : angle       2.38210 (    3)
  link_NAG-ASN         : bond        0.00525 (    4)
  link_NAG-ASN         : angle       3.32173 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.6992 (t80) cc_final: 0.6606 (t80)
REVERT: A  412 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7514 (mp)
REVERT: A  662 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7307 (tmm-80)
REVERT: A 1019 PHE cc_start: 0.8151 (m-80) cc_final: 0.7905 (m-80)
REVERT: A 1068 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7100 (tt0)
REVERT: A 1075 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7291 (ttt90)
REVERT: A 1156 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.5479 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 100
  average time/residue: 1.2123
  time to fit residues: 128.4832
Evaluate side-chains
  104 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  658 SER
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  842 HIS
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1068 GLU
Chi-restraints excluded: chain A residue 1075 ARG
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1156 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 50 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   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 954 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.149265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.125621 restraints weight = 20467.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.46
r_work: 0.3351 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6906  Z= 0.143
  Angle     :  0.535   6.772   9403  Z= 0.283
  Chirality :  0.039   0.187   1095
  Planarity :  0.004   0.064   1163
  Dihedral  :  6.499  58.844   1062
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.95 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.78 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.30), residues: 819
  helix:  1.28 (0.23), residues: 499
  sheet:  1.36 (0.75), residues: 43
  loop :  1.25 (0.42), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 468 
 TYR   0.013   0.001   TYR A 711 
 PHE   0.019   0.001   PHE A 505 
 TRP   0.013   0.001   TRP A 415 
 HIS   0.004   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6895)
  covalent geometry    : angle       0.52334 ( 9376)
  SS BOND              : bond        0.00131 (    6)
  SS BOND              : angle       0.41457 (   12)
  hydrogen bonds       : bond        0.04747 (  405)
  hydrogen bonds       : angle       4.98780 ( 1173)
  link_BETA1-4         : bond        0.00030 (    1)
  link_BETA1-4         : angle       2.31727 (    3)
  link_NAG-ASN         : bond        0.00485 (    4)
  link_NAG-ASN         : angle       2.94444 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.6974 (t80) cc_final: 0.6596 (t80)
REVERT: A  412 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7520 (mp)
REVERT: A  662 ARG cc_start: 0.7583 (ptp90) cc_final: 0.7306 (tmm-80)
REVERT: A 1019 PHE cc_start: 0.8114 (m-80) cc_final: 0.7909 (m-80)
REVERT: A 1068 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7058 (tt0)
REVERT: A 1075 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7257 (ttt90)
REVERT: A 1122 GLN cc_start: 0.8086 (tp40) cc_final: 0.7771 (tp-100)
REVERT: A 1156 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.5467 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 100
  average time/residue: 1.1455
  time to fit residues: 121.6483
Evaluate side-chains
  103 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  658 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  842 HIS
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1068 GLU
Chi-restraints excluded: chain A residue 1075 ARG
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1156 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0970
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 954 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.149232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.125880 restraints weight = 20454.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.44
r_work: 0.3360 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6906  Z= 0.140
  Angle     :  0.532   6.603   9403  Z= 0.282
  Chirality :  0.039   0.187   1095
  Planarity :  0.005   0.091   1163
  Dihedral  :  6.435  58.713   1062
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.71 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.32 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.30), residues: 819
  helix:  1.32 (0.23), residues: 499
  sheet:  1.46 (0.75), residues: 43
  loop :  1.27 (0.43), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 468 
 TYR   0.013   0.001   TYR A 711 
 PHE   0.019   0.001   PHE A 505 
 TRP   0.013   0.001   TRP A 415 
 HIS   0.003   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6895)
  covalent geometry    : angle       0.52074 ( 9376)
  SS BOND              : bond        0.00128 (    6)
  SS BOND              : angle       0.40275 (   12)
  hydrogen bonds       : bond        0.04675 (  405)
  hydrogen bonds       : angle       4.96079 ( 1173)
  link_BETA1-4         : bond        0.00007 (    1)
  link_BETA1-4         : angle       2.27038 (    3)
  link_NAG-ASN         : bond        0.00475 (    4)
  link_NAG-ASN         : angle       2.87152 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.6968 (t80) cc_final: 0.6583 (t80)
REVERT: A  412 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7518 (mp)
REVERT: A  662 ARG cc_start: 0.7576 (ptp90) cc_final: 0.7316 (tmm-80)
REVERT: A 1068 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7046 (tt0)
REVERT: A 1075 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7203 (ttt90)
REVERT: A 1122 GLN cc_start: 0.8141 (tp40) cc_final: 0.7725 (tp-100)
  outliers start: 17
  outliers final: 10
  residues processed: 104
  average time/residue: 1.1434
  time to fit residues: 126.3110
Evaluate side-chains
  104 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  658 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  842 HIS
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1068 GLU
Chi-restraints excluded: chain A residue 1075 ARG
Chi-restraints excluded: chain A residue 1125 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0470
   chunk 42 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
A 954 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.149252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.125959 restraints weight = 20480.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.44
r_work: 0.3359 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6906  Z= 0.141
  Angle     :  0.531   6.585   9403  Z= 0.281
  Chirality :  0.039   0.186   1095
  Planarity :  0.005   0.090   1163
  Dihedral  :  6.417  58.819   1062
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.71 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 17.72 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.30), residues: 819
  helix:  1.34 (0.23), residues: 499
  sheet:  1.47 (0.75), residues: 43
  loop :  1.28 (0.43), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 468 
 TYR   0.013   0.001   TYR A 711 
 PHE   0.019   0.001   PHE A 505 
 TRP   0.013   0.001   TRP A 415 
 HIS   0.003   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6895)
  covalent geometry    : angle       0.51993 ( 9376)
  SS BOND              : bond        0.00130 (    6)
  SS BOND              : angle       0.39908 (   12)
  hydrogen bonds       : bond        0.04645 (  405)
  hydrogen bonds       : angle       4.94502 ( 1173)
  link_BETA1-4         : bond        0.00021 (    1)
  link_BETA1-4         : angle       2.26225 (    3)
  link_NAG-ASN         : bond        0.00469 (    4)
  link_NAG-ASN         : angle       2.86784 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.6929 (t80) cc_final: 0.6526 (t80)
REVERT: A  412 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7527 (mp)
REVERT: A  662 ARG cc_start: 0.7577 (ptp90) cc_final: 0.7318 (tmm-80)
REVERT: A 1075 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7219 (ttt90)
REVERT: A 1122 GLN cc_start: 0.8120 (tp40) cc_final: 0.7689 (tp-100)
  outliers start: 14
  outliers final: 10
  residues processed: 102
  average time/residue: 1.2238
  time to fit residues: 132.2716
Evaluate side-chains
  104 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  513 ASN
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  658 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  842 HIS
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1075 ARG
Chi-restraints excluded: chain A residue 1125 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0470
   chunk 62 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0980
   chunk 35 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.2278

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

Flipped N/Q/H residues before XYZ refinement:
A 954 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.152285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.129395 restraints weight = 20526.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.44
r_work: 0.3406 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6906  Z= 0.102
  Angle     :  0.491   4.767   9403  Z= 0.261
  Chirality :  0.038   0.204   1095
  Planarity :  0.004   0.086   1163
  Dihedral  :  6.037  59.457   1062
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.12 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.31), residues: 819
  helix:  1.56 (0.23), residues: 499
  sheet:  1.80 (0.76), residues: 43
  loop :  1.40 (0.43), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 468 
 TYR   0.012   0.001   TYR A 711 
 PHE   0.029   0.001   PHE A 634 
 TRP   0.013   0.001   TRP A 415 
 HIS   0.003   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 6895)
  covalent geometry    : angle       0.48457 ( 9376)
  SS BOND              : bond        0.00099 (    6)
  SS BOND              : angle       0.30527 (   12)
  hydrogen bonds       : bond        0.04036 (  405)
  hydrogen bonds       : angle       4.80738 ( 1173)
  link_BETA1-4         : bond        0.00041 (    1)
  link_BETA1-4         : angle       2.01013 (    3)
  link_NAG-ASN         : bond        0.00456 (    4)
  link_NAG-ASN         : angle       2.15969 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5157.42 seconds
wall clock time: 88 minutes 1.34 seconds (5281.34 seconds total)