Starting phenix.real_space_refine
on Wed Sep 17 08:22:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgj_50408/09_2025/9fgj_50408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgj_50408/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgj_50408/09_2025/9fgj_50408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgj_50408/09_2025/9fgj_50408.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fgj_50408/09_2025/9fgj_50408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgj_50408/09_2025/9fgj_50408.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.031
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.92, per 1000 atoms: 0.27
  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: 0.58
  Conformation dependent library (CDL) restraints added in 431.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.25
  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: 1.10

  Time building geometry restraints manager: 0.79 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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.530
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.450
-------------------------------------------------------------------------------
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 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:  1.53 (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
 ARG   0.006   0.000   ARG A 690 
 TYR   0.032   0.001   TYR A 908 
 PHE   0.023   0.001   PHE A 551 
 TRP   0.005   0.001   TRP A 403 
 HIS   0.004   0.001   HIS A 248 

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

*********************** 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  : 0.291 
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: 0.1121
  time to fit residues: 9.8422
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  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3891 r_free = 0.3891 target = 0.127573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.087654 restraints weight = 14758.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.091261 restraints weight = 8304.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.093731 restraints weight = 5844.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.095335 restraints weight = 4654.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.096461 restraints weight = 4014.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
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      :  0.004   0.051   7152  Z= 0.160
  Angle     :  0.571   7.691   9664  Z= 0.298
  Chirality :  0.041   0.197   1080
  Planarity :  0.005   0.047   1268
  Dihedral  :  4.550  18.392    944
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.70 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.54 (0.29), residues: 881
  helix:  1.94 (0.23), residues: 488
  sheet: -0.53 (0.66), residues: 45
  loop : -0.01 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 664 
 TYR   0.023   0.001   TYR A 550 
 PHE   0.020   0.001   PHE A 551 
 TRP   0.005   0.001   TRP A 714 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7151)
  covalent geometry    : angle       0.57083 ( 9662)
  SS BOND              : bond        0.00244 (    1)
  SS BOND              : angle       1.56955 (    2)
  hydrogen bonds       : bond        0.05118 (  384)
  hydrogen bonds       : angle       4.23271 ( 1104)

*********************** 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
  71 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  701 MET cc_start: 0.7594 (mmm) cc_final: 0.7375 (mmm)
REVERT: A  740 LEU cc_start: 0.8760 (tp) cc_final: 0.8543 (tp)
  outliers start: 10
  outliers final: 5
  residues processed: 70
  average time/residue: 0.0972
  time to fit residues: 9.1395
Evaluate side-chains
  54 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  776 ILE
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 48 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 27 optimal weight:    0.1980
   chunk 59 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.3866 r_free = 0.3866 target = 0.125571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.084402 restraints weight = 15403.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.087620 restraints weight = 9333.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.089824 restraints weight = 6863.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.091270 restraints weight = 5640.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.092222 restraints weight = 4991.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7152  Z= 0.226
  Angle     :  0.629   7.751   9664  Z= 0.325
  Chirality :  0.042   0.160   1080
  Planarity :  0.005   0.046   1268
  Dihedral  :  4.652  16.876    944
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  9.87 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.45 (0.29), residues: 881
  helix:  1.89 (0.23), residues: 488
  sheet: -0.63 (0.68), residues: 43
  loop : -0.08 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 690 
 TYR   0.022   0.002   TYR A 256 
 PHE   0.020   0.002   PHE A 835 
 TRP   0.005   0.001   TRP A 687 
 HIS   0.006   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 7151)
  covalent geometry    : angle       0.62823 ( 9662)
  SS BOND              : bond        0.00255 (    1)
  SS BOND              : angle       1.92997 (    2)
  hydrogen bonds       : bond        0.05640 (  384)
  hydrogen bonds       : angle       4.31260 ( 1104)

*********************** 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
  71 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.7986 (tp30) cc_final: 0.7561 (tm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 69
  average time/residue: 0.0906
  time to fit residues: 8.6913
Evaluate side-chains
  59 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  395 ILE
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0050
   chunk 2 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0870
   chunk 73 optimal weight:    8.9990
   overall best weight:    0.4172

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

Flipped N/Q/H residues before XYZ refinement:
A 413 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.132574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.092829 restraints weight = 15272.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.096284 restraints weight = 9046.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098638 restraints weight = 6573.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.100087 restraints weight = 5354.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.101171 restraints weight = 4711.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   7152  Z= 0.113
  Angle     :  0.528   8.285   9664  Z= 0.271
  Chirality :  0.039   0.181   1080
  Planarity :  0.004   0.049   1268
  Dihedral  :  4.276  16.609    944
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.43 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.72 (0.29), residues: 881
  helix:  2.13 (0.23), residues: 488
  sheet: -0.76 (0.69), residues: 45
  loop :  0.04 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 690 
 TYR   0.025   0.001   TYR A 550 
 PHE   0.021   0.001   PHE A 551 
 TRP   0.004   0.001   TRP A 403 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7151)
  covalent geometry    : angle       0.52749 ( 9662)
  SS BOND              : bond        0.00272 (    1)
  SS BOND              : angle       1.49632 (    2)
  hydrogen bonds       : bond        0.04191 (  384)
  hydrogen bonds       : angle       3.95588 ( 1104)

*********************** 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
  68 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.7855 (tp30) cc_final: 0.7367 (tm-30)
REVERT: A  419 ASP cc_start: 0.8695 (t70) cc_final: 0.8308 (t70)
  outliers start: 8
  outliers final: 5
  residues processed: 68
  average time/residue: 0.1022
  time to fit residues: 9.3251
Evaluate side-chains
  56 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
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  498 VAL
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  849 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 76 optimal weight:   30.0000
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 413 ASN
A 703 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.136630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.102030 restraints weight = 15338.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.105425 restraints weight = 10083.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.106286 restraints weight = 6622.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.106753 restraints weight = 5993.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.107425 restraints weight = 5578.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1801

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= 0.150
  Angle     :  0.556   9.049   9664  Z= 0.282
  Chirality :  0.041   0.300   1080
  Planarity :  0.004   0.051   1268
  Dihedral  :  4.248  16.578    944
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.95 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 (0.29), residues: 881
  helix:  2.16 (0.23), residues: 489
  sheet: -0.69 (0.71), residues: 45
  loop :  0.10 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 690 
 TYR   0.024   0.001   TYR A 550 
 PHE   0.020   0.001   PHE A 551 
 TRP   0.005   0.001   TRP A 687 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7151)
  covalent geometry    : angle       0.55597 ( 9662)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       1.50260 (    2)
  hydrogen bonds       : bond        0.04587 (  384)
  hydrogen bonds       : angle       4.02634 ( 1104)

*********************** 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
  62 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.8033 (tp30) cc_final: 0.7587 (tm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0968
  time to fit residues: 8.2369
Evaluate side-chains
  55 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  681 VAL
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 43 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 39 optimal weight:    0.1980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 413 ASN
A 703 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.138211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.103847 restraints weight = 15525.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.107184 restraints weight = 10181.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.108266 restraints weight = 6849.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.108604 restraints weight = 5897.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.108699 restraints weight = 5537.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1953

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= 0.119
  Angle     :  0.543  10.698   9664  Z= 0.271
  Chirality :  0.040   0.312   1080
  Planarity :  0.004   0.052   1268
  Dihedral  :  4.121  16.473    944
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.47 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.90 (0.29), residues: 881
  helix:  2.24 (0.24), residues: 490
  sheet: -0.53 (0.73), residues: 45
  loop :  0.16 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1180 
 TYR   0.026   0.001   TYR A 550 
 PHE   0.019   0.001   PHE A 551 
 TRP   0.004   0.001   TRP A 403 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7151)
  covalent geometry    : angle       0.54277 ( 9662)
  SS BOND              : bond        0.00280 (    1)
  SS BOND              : angle       1.42767 (    2)
  hydrogen bonds       : bond        0.04155 (  384)
  hydrogen bonds       : angle       3.91273 ( 1104)

*********************** 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
  64 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.8004 (tp30) cc_final: 0.7575 (tm-30)
REVERT: A  882 ASP cc_start: 0.7195 (m-30) cc_final: 0.6980 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0924
  time to fit residues: 8.0530
Evaluate side-chains
  56 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  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  819 THR
Chi-restraints excluded: chain A residue  849 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 75 optimal weight:   20.0000
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 413 ASN
A 703 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.134086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.095174 restraints weight = 15437.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.098575 restraints weight = 9288.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.100822 restraints weight = 6807.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.102353 restraints weight = 5576.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.103182 restraints weight = 4901.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7152  Z= 0.226
  Angle     :  0.633  10.405   9664  Z= 0.319
  Chirality :  0.043   0.290   1080
  Planarity :  0.004   0.051   1268
  Dihedral  :  4.399  16.549    944
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.86 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.73 (0.29), residues: 881
  helix:  2.10 (0.23), residues: 489
  sheet: -0.58 (0.74), residues: 43
  loop :  0.06 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1180 
 TYR   0.017   0.002   TYR A 256 
 PHE   0.020   0.002   PHE A 835 
 TRP   0.007   0.001   TRP A 687 
 HIS   0.005   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 7151)
  covalent geometry    : angle       0.63227 ( 9662)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       1.82156 (    2)
  hydrogen bonds       : bond        0.05333 (  384)
  hydrogen bonds       : angle       4.22447 ( 1104)

*********************** 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
  66 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.8130 (tp30) cc_final: 0.7668 (tm-30)
REVERT: A 1052 GLN cc_start: 0.8559 (mt0) cc_final: 0.8243 (mp-120)
  outliers start: 17
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0935
  time to fit residues: 8.4128
Evaluate side-chains
  54 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  650 LEU
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
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 59 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 413 ASN
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 = 0.4043 r_free = 0.4043 target = 0.135521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.096401 restraints weight = 15455.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.099866 restraints weight = 9255.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.102201 restraints weight = 6763.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.103621 restraints weight = 5537.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.104681 restraints weight = 4876.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2188

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= 0.131
  Angle     :  0.561   9.280   9664  Z= 0.283
  Chirality :  0.040   0.253   1080
  Planarity :  0.004   0.052   1268
  Dihedral  :  4.196  16.345    944
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.90 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 (0.29), residues: 881
  helix:  2.19 (0.24), residues: 489
  sheet: -0.41 (0.75), residues: 43
  loop :  0.10 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1180 
 TYR   0.027   0.001   TYR A 550 
 PHE   0.020   0.001   PHE A 551 
 TRP   0.004   0.001   TRP A 403 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7151)
  covalent geometry    : angle       0.56070 ( 9662)
  SS BOND              : bond        0.00285 (    1)
  SS BOND              : angle       1.58528 (    2)
  hydrogen bonds       : bond        0.04367 (  384)
  hydrogen bonds       : angle       4.00558 ( 1104)

*********************** 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
  62 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.8034 (tp30) cc_final: 0.7585 (tm-30)
REVERT: A  726 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.7266 (mpp80)
  outliers start: 13
  outliers final: 8
  residues processed: 61
  average time/residue: 0.0965
  time to fit residues: 8.1201
Evaluate side-chains
  56 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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  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 68 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 413 ASN
A 703 HIS
** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.137150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.102511 restraints weight = 15429.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.105914 restraints weight = 10773.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.106847 restraints weight = 6865.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.107204 restraints weight = 6047.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.107654 restraints weight = 5394.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7152  Z= 0.132
  Angle     :  0.554   8.072   9664  Z= 0.278
  Chirality :  0.040   0.228   1080
  Planarity :  0.004   0.053   1268
  Dihedral  :  4.137  16.233    944
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 14.42 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.88 (0.29), residues: 881
  helix:  2.19 (0.24), residues: 490
  sheet: -0.33 (0.75), residues: 43
  loop :  0.15 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1180 
 TYR   0.026   0.001   TYR A 550 
 PHE   0.020   0.001   PHE A 551 
 TRP   0.004   0.001   TRP A 403 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7151)
  covalent geometry    : angle       0.55362 ( 9662)
  SS BOND              : bond        0.00276 (    1)
  SS BOND              : angle       1.50620 (    2)
  hydrogen bonds       : bond        0.04328 (  384)
  hydrogen bonds       : angle       4.00065 ( 1104)

*********************** 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
  55 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.8053 (tp30) cc_final: 0.7609 (tm-30)
REVERT: A  908 TYR cc_start: 0.6345 (p90) cc_final: 0.6129 (p90)
  outliers start: 7
  outliers final: 7
  residues processed: 55
  average time/residue: 0.0989
  time to fit residues: 7.4693
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  : 0.294 
-------------------------------------------------------------------------------
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  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 86 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 42 optimal weight:    0.4980
   chunk 10 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 413 ASN
A 703 HIS
** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.136765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.102203 restraints weight = 15284.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.105502 restraints weight = 10681.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.107163 restraints weight = 6912.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.107253 restraints weight = 5671.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.107730 restraints weight = 5595.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7152  Z= 0.148
  Angle     :  0.575   9.979   9664  Z= 0.288
  Chirality :  0.041   0.217   1080
  Planarity :  0.004   0.053   1268
  Dihedral  :  4.160  17.059    944
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 14.42 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.87 (0.29), residues: 881
  helix:  2.17 (0.24), residues: 491
  sheet: -0.35 (0.74), residues: 43
  loop :  0.17 (0.36), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1180 
 TYR   0.026   0.001   TYR A 550 
 PHE   0.020   0.001   PHE A 551 
 TRP   0.004   0.001   TRP A 403 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7151)
  covalent geometry    : angle       0.57449 ( 9662)
  SS BOND              : bond        0.00264 (    1)
  SS BOND              : angle       1.52049 (    2)
  hydrogen bonds       : bond        0.04448 (  384)
  hydrogen bonds       : angle       4.03512 ( 1104)

********************** 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
  56 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 GLU cc_start: 0.8076 (tp30) cc_final: 0.7630 (tm-30)
REVERT: A  741 MET cc_start: 0.7802 (mmt) cc_final: 0.7492 (mmt)
REVERT: A  853 MET cc_start: 0.7904 (mpp) cc_final: 0.7689 (ptp)
REVERT: A  908 TYR cc_start: 0.6405 (p90) cc_final: 0.6171 (p90)
  outliers start: 9
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0975
  time to fit residues: 7.3741
Evaluate side-chains
  54 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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  650 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  808 SER
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 83 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 71 optimal weight:    7.9990
   chunk 17 optimal weight:    0.1980
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 46 optimal weight:    7.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 413 ASN
A 614 ASN
A 703 HIS
** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.136688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.097996 restraints weight = 15309.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.101599 restraints weight = 9146.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.103917 restraints weight = 6640.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.105524 restraints weight = 5412.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.106574 restraints weight = 4728.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7152  Z= 0.121
  Angle     :  0.571   9.927   9664  Z= 0.285
  Chirality :  0.040   0.211   1080
  Planarity :  0.004   0.055   1268
  Dihedral  :  4.043  14.461    944
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 14.94 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.97 (0.29), residues: 881
  helix:  2.25 (0.24), residues: 490
  sheet: -0.15 (0.75), residues: 43
  loop :  0.20 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1180 
 TYR   0.027   0.001   TYR A 550 
 PHE   0.019   0.001   PHE A 551 
 TRP   0.004   0.001   TRP A 403 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7151)
  covalent geometry    : angle       0.57095 ( 9662)
  SS BOND              : bond        0.00295 (    1)
  SS BOND              : angle       1.44352 (    2)
  hydrogen bonds       : bond        0.04127 (  384)
  hydrogen bonds       : angle       3.95191 ( 1104)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1417.21 seconds
wall clock time: 25 minutes 16.78 seconds (1516.78 seconds total)