Starting phenix.real_space_refine
on Thu Jun  4 10:18:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xd4_66754/06_2026/9xd4_66754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xd4_66754/06_2026/9xd4_66754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xd4_66754/06_2026/9xd4_66754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xd4_66754/06_2026/9xd4_66754.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xd4_66754/06_2026/9xd4_66754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xd4_66754/06_2026/9xd4_66754.cif"
  }
  resolution = 2.79
  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=   0.027
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
     Zn      1      6.06       5
     S      85      5.16       5
     C    7465      2.51       5
     N    2032      2.21       5
     O    2214      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11797
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 11796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1477, 11796
          Classifications: {'peptide': 1477}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1432}
          Chain breaks: 14
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    809  SG  CYS A1028      38.182  95.176  35.858  1.00 68.93           S
  ATOM    828  SG  CYS A1031      41.082  97.452  35.517  1.00 99.80           S
  ATOM   1071  SG  CYS A1062      38.296  98.759  37.510  1.00 76.83           S
  ATOM   1091  SG  CYS A1065      40.063  96.058  39.094  1.00 77.96           S

  Time building chain proxies: 2.82, per 1000 atoms: 0.24
  Number of scatterers: 11797
  At special positions: 0
  Unit cell: (110.376, 113.88, 127.896, 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)
     Zn      1     29.99
     S      85     16.00
     O    2214      8.00
     N    2032      7.00
     C    7465      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 586.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A4001 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1062 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1031 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1065 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1028 "
      Number of angles added : 6


  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2830

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 10 sheets defined
      60.9% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 930 through 942
    Processing helix  chain 'A' and resid 942 through 946
    Processing helix  chain 'A' and resid 955 through 967
    Processing helix  chain 'A' and resid 973 through 987
    Processing helix  chain 'A' and resid 987 through 997
    Processing helix  chain 'A' and resid 1008 through 1024
    Processing helix  chain 'A' and resid 1028 through 1041
    Processing helix  chain 'A' and resid 1044 through 1057
      removed outlier: 3.708A  pdb=" N   GLN A1057 " --> pdb=" O   ALA A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1061
      removed outlier: 3.533A  pdb=" N   HIS A1061 " --> pdb=" O   LEU A1058 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1058 through 1061'
    Processing helix  chain 'A' and resid 1078 through 1082
    Processing helix  chain 'A' and resid 1084 through 1088
      removed outlier: 3.717A  pdb=" N   VAL A1088 " --> pdb=" O   ILE A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1105 through 1111
      removed outlier: 3.603A  pdb=" N   ARG A1111 " --> pdb=" O   ASP A1107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1139
      removed outlier: 3.587A  pdb=" N   SER A1139 " --> pdb=" O   MET A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1175 through 1186
    Processing helix  chain 'A' and resid 1196 through 1208
    Processing helix  chain 'A' and resid 1221 through 1232
      removed outlier: 3.510A  pdb=" N   LEU A1225 " --> pdb=" O   PRO A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1281
      removed outlier: 3.529A  pdb=" N   CYS A1273 " --> pdb=" O   GLU A1269 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLN A1277 " --> pdb=" O   CYS A1273 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   PHE A1279 " --> pdb=" O   ASP A1275 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LYS A1280 " --> pdb=" O   VAL A1276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1291 through 1296
      removed outlier: 3.777A  pdb=" N   ILE A1295 " --> pdb=" O   GLN A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1297 through 1309
    Processing helix  chain 'A' and resid 1315 through 1328
    Processing helix  chain 'A' and resid 1330 through 1348
    Processing helix  chain 'A' and resid 1401 through 1426
      removed outlier: 3.688A  pdb=" N   LEU A1407 " --> pdb=" O   ARG A1403 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   LEU A1412 " --> pdb=" O   GLY A1408 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   TYR A1413 " --> pdb=" O   SER A1409 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLN A1424 " --> pdb=" O   ILE A1420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1429 through 1435
      removed outlier: 3.645A  pdb=" N   ASN A1433 " --> pdb=" O   GLU A1430 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   VAL A1435 " --> pdb=" O   ILE A1432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1436 through 1463
    Processing helix  chain 'A' and resid 1465 through 1481
      removed outlier: 3.655A  pdb=" N   SER A1469 " --> pdb=" O   ARG A1465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1487 through 1505
    Processing helix  chain 'A' and resid 1507 through 1514
      removed outlier: 4.054A  pdb=" N   ASN A1514 " --> pdb=" O   ASN A1510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1524
    Processing helix  chain 'A' and resid 1524 through 1531
    Processing helix  chain 'A' and resid 1532 through 1534
      No H-bonds generated for 'chain 'A' and resid 1532 through 1534'
    Processing helix  chain 'A' and resid 1543 through 1547
    Processing helix  chain 'A' and resid 1552 through 1572
      removed outlier: 4.663A  pdb=" N   ASP A1572 " --> pdb=" O   CYS A1568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1572 through 1581
      removed outlier: 4.043A  pdb=" N   LYS A1581 " --> pdb=" O   VAL A1577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1603 through 1612
    Processing helix  chain 'A' and resid 1631 through 1651
    Processing helix  chain 'A' and resid 1758 through 1773
    Processing helix  chain 'A' and resid 1780 through 1792
    Processing helix  chain 'A' and resid 1793 through 1795
      No H-bonds generated for 'chain 'A' and resid 1793 through 1795'
    Processing helix  chain 'A' and resid 1796 through 1805
    Processing helix  chain 'A' and resid 2295 through 2305
    Processing helix  chain 'A' and resid 2317 through 2336
      removed outlier: 3.876A  pdb=" N   LEU A2322 " --> pdb=" O   LYS A2318 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ASN A2323 " --> pdb=" O   GLU A2319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2367 through 2379
      removed outlier: 3.511A  pdb=" N   GLY A2373 " --> pdb=" O   SER A2369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2382 through 2397
      removed outlier: 4.178A  pdb=" N   PHE A2388 " --> pdb=" O   ASP A2384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2447 through 2455
    Processing helix  chain 'A' and resid 2476 through 2503
      removed outlier: 3.543A  pdb=" N   SER A2481 " --> pdb=" O   HIS A2477 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   VAL A2489 " --> pdb=" O   SER A2485 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU A2490 " --> pdb=" O   LEU A2486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2530 through 2558
      removed outlier: 5.055A  pdb=" N   TRP A2542 " --> pdb=" O   ASP A2538 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   LYS A2543 " --> pdb=" O   GLU A2539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2589 through 2594
      removed outlier: 3.614A  pdb=" N   MET A2594 " --> pdb=" O   ILE A2591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2595 through 2600
      removed outlier: 3.520A  pdb=" N   ILE A2599 " --> pdb=" O   PHE A2595 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASN A2600 " --> pdb=" O   THR A2596 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2595 through 2600'
    Processing helix  chain 'A' and resid 2605 through 2623
    Processing helix  chain 'A' and resid 2626 through 2645
      removed outlier: 3.765A  pdb=" N   PHE A2641 " --> pdb=" O   ARG A2637 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   HIS A2644 " --> pdb=" O   ILE A2640 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL A2645 " --> pdb=" O   PHE A2641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2645 through 2652
    Processing helix  chain 'A' and resid 2652 through 2657
    Processing helix  chain 'A' and resid 2658 through 2659
      No H-bonds generated for 'chain 'A' and resid 2658 through 2659'
    Processing helix  chain 'A' and resid 2660 through 2664
      removed outlier: 3.712A  pdb=" N   GLY A2664 " --> pdb=" O   SER A2661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2670 through 2675
      removed outlier: 3.647A  pdb=" N   VAL A2675 " --> pdb=" O   TYR A2671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2678 through 2697
    Processing helix  chain 'A' and resid 2753 through 2764
    Processing helix  chain 'A' and resid 2771 through 2783
    Processing helix  chain 'A' and resid 2801 through 2805
    Processing helix  chain 'A' and resid 2806 through 2816
    Processing helix  chain 'A' and resid 2818 through 2836
    Processing helix  chain 'A' and resid 2900 through 2909
    Processing helix  chain 'A' and resid 2993 through 3003
    Processing helix  chain 'A' and resid 3043 through 3060
    Processing helix  chain 'A' and resid 3062 through 3073
    Processing helix  chain 'A' and resid 3091 through 3094
    Processing helix  chain 'A' and resid 3095 through 3100
      removed outlier: 3.635A  pdb=" N   VAL A3099 " --> pdb=" O   ALA A3095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3104 through 3112
      removed outlier: 3.791A  pdb=" N   LEU A3112 " --> pdb=" O   VAL A3108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3116 through 3121
      removed outlier: 3.992A  pdb=" N   VAL A3121 " --> pdb=" O   ALA A3117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3131 through 3141
    Processing helix  chain 'A' and resid 3142 through 3159
      removed outlier: 3.561A  pdb=" N   PHE A3146 " --> pdb=" O   PHE A3142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3170 through 3185
      removed outlier: 4.025A  pdb=" N   MET A3184 " --> pdb=" O   LEU A3180 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ILE A3185 " --> pdb=" O   LEU A3181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3208 through 3217
      removed outlier: 3.708A  pdb=" N   LEU A3212 " --> pdb=" O   THR A3208 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL A3213 " --> pdb=" O   VAL A3209 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE A3217 " --> pdb=" O   VAL A3213 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 947 through 948
      removed outlier: 3.980A  pdb=" N   LEU A 952 " --> pdb=" O   ARG A 948 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 971 through 972
      removed outlier: 6.729A  pdb=" N   VAL A 971 " --> pdb=" O   TYR A1755 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1003 through 1004
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1143 through 1145
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1357 through 1362
      removed outlier: 3.903A  pdb=" N   GLY A1357 " --> pdb=" O   LEU A1374 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU A1383 " --> pdb=" O   LYS A1373 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   LEU A1386 " --> pdb=" O   GLY A1396 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   GLY A1396 " --> pdb=" O   LEU A1386 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2506 through 2511
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2574 through 2576
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3005 through 3009
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3078 through 3081
      removed outlier: 3.974A  pdb=" N   SER A3078 " --> pdb=" O   ARG A3224 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3086 through 3089

    633 hydrogen bonds defined for protein.
    1833 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: 2.05

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3839
        1.34 -     1.46: 2319
        1.46 -     1.58: 5709
        1.58 -     1.70: 0
        1.70 -     1.81: 123
  Bond restraints: 11990
  Sorted by residual:
  bond pdb=" C   VAL A1288 "
       pdb=" N   PRO A1289 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.034 2.34e-02 1.83e+03 2.05e+00
  bond pdb=" CG  ARG A1307 "
       pdb=" CD  ARG A1307 "
    ideal  model  delta    sigma   weight residual
    1.520  1.481  0.039 3.00e-02 1.11e+03 1.70e+00
  bond pdb=" CB  VAL A1614 "
       pdb=" CG1 VAL A1614 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.22e+00
  bond pdb=" CB  ARG A1307 "
       pdb=" CG  ARG A1307 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.10e+00
  bond pdb=" CB  ARG A3173 "
       pdb=" CG  ARG A3173 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.04e+00
  ... (remaining 11985 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 15890
        1.99 -     3.99: 220
        3.99 -     5.98: 40
        5.98 -     7.97: 6
        7.97 -     9.96: 2
  Bond angle restraints: 16158
  Sorted by residual:
  angle pdb=" C   ARG A1659 "
        pdb=" N   THR A1660 "
        pdb=" CA  THR A1660 "
      ideal   model   delta    sigma   weight residual
     121.54  127.90   -6.36 1.91e+00 2.74e-01 1.11e+01
  angle pdb=" C   ASN A1007 "
        pdb=" N   ILE A1008 "
        pdb=" CA  ILE A1008 "
      ideal   model   delta    sigma   weight residual
     121.97  127.81   -5.84 1.80e+00 3.09e-01 1.05e+01
  angle pdb=" C   ASP A1657 "
        pdb=" N   THR A1658 "
        pdb=" CA  THR A1658 "
      ideal   model   delta    sigma   weight residual
     121.54  127.19   -5.65 1.91e+00 2.74e-01 8.74e+00
  angle pdb=" C   PRO A3123 "
        pdb=" N   THR A3124 "
        pdb=" CA  THR A3124 "
      ideal   model   delta    sigma   weight residual
     121.54  127.07   -5.53 1.91e+00 2.74e-01 8.39e+00
  angle pdb=" CA  LEU A3168 "
        pdb=" CB  LEU A3168 "
        pdb=" CG  LEU A3168 "
      ideal   model   delta    sigma   weight residual
     116.30  126.26   -9.96 3.50e+00 8.16e-02 8.11e+00
  ... (remaining 16153 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.22: 6745
       15.22 -    30.45: 511
       30.45 -    45.67: 90
       45.67 -    60.90: 6
       60.90 -    76.12: 7
  Dihedral angle restraints: 7359
    sinusoidal: 3022
      harmonic: 4337
  Sorted by residual:
  dihedral pdb=" CA  THR A2455 "
           pdb=" C   THR A2455 "
           pdb=" N   THR A2456 "
           pdb=" CA  THR A2456 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.87   23.13     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  ASN A2623 "
           pdb=" C   ASN A2623 "
           pdb=" N   SER A2624 "
           pdb=" CA  SER A2624 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.51   17.49     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  PHE A1505 "
           pdb=" C   PHE A1505 "
           pdb=" N   LEU A1506 "
           pdb=" CA  LEU A1506 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.87  -17.13     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 7356 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1002
       0.029 -    0.058: 569
       0.058 -    0.087: 199
       0.087 -    0.117: 71
       0.117 -    0.146: 21
  Chirality restraints: 1862
  Sorted by residual:
  chirality pdb=" CA  PHE A2633 "
            pdb=" N   PHE A2633 "
            pdb=" C   PHE A2633 "
            pdb=" CB  PHE A2633 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CB  THR A2587 "
            pdb=" CA  THR A2587 "
            pdb=" OG1 THR A2587 "
            pdb=" CG2 THR A2587 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  TRP A2542 "
            pdb=" N   TRP A2542 "
            pdb=" C   TRP A2542 "
            pdb=" CB  TRP A2542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.12e-01
  ... (remaining 1859 not shown)

  Planarity restraints: 2045
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A2633 "   -0.018 2.00e-02 2.50e+03   1.77e-02 5.47e+00
        pdb=" CG  PHE A2633 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE A2633 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A2633 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A2633 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A2633 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A2633 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A1286 "   -0.038 5.00e-02 4.00e+02   5.75e-02 5.30e+00
        pdb=" N   PRO A1287 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A1287 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A1287 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A2503 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.66e+00
        pdb=" N   PRO A2504 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A2504 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A2504 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 2042 not shown)

  Histogram of nonbonded interaction distances:
        2.62 -     3.07: 7828
        3.07 -     3.53: 12341
        3.53 -     3.99: 18622
        3.99 -     4.44: 23256
        4.44 -     4.90: 34792
  Nonbonded interactions: 96839
  Sorted by model distance:
  nonbonded pdb=" N   SER A2515 "
            pdb=" O   SER A2515 "
     model   vdw
     2.615 2.496
  nonbonded pdb=" N   THR A1660 "
            pdb=" N   ALA A1661 "
     model   vdw
     2.623 2.560
  nonbonded pdb=" N   SER A2341 "
            pdb=" O   SER A2341 "
     model   vdw
     2.631 2.496
  nonbonded pdb=" N   VAL A1537 "
            pdb=" O   VAL A1537 "
     model   vdw
     2.633 2.496
  nonbonded pdb=" N   GLN A1291 "
            pdb=" O   GLN A1291 "
     model   vdw
     2.644 2.496
  ... (remaining 96834 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 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:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.720
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
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      :  0.004   0.039  11994  Z= 0.167
  Angle     :  0.635   9.965  16164  Z= 0.324
  Chirality :  0.042   0.146   1862
  Planarity :  0.005   0.058   2045
  Dihedral  : 11.048  76.120   4529
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.21), residues: 1447
  helix:  0.33 (0.17), residues: 825
  sheet: -0.55 (0.61), residues: 80
  loop : -1.31 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A2585 
 TYR   0.019   0.002   TYR A1130 
 PHE   0.041   0.002   PHE A2633 
 TRP   0.020   0.002   TRP A2542 
 HIS   0.003   0.001   HIS A3045 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.17 (11990)
  covalent geometry    : angle       0.62393 /  0.32 (16158)
  hydrogen bonds       : bond        0.12900 /  8.61 (  633)
  hydrogen bonds       : angle       5.89295 /  4.17 ( 1833)
  metal coordination   : bond        0.00856 /  0.50 (    4)
  metal coordination   : angle       6.06224 /  4.11 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 367
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: A  942 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8352 (ttpp)
REVERT: A 1001 LYS cc_start: 0.8709 (pttt) cc_final: 0.8489 (ptmt)
REVERT: A 1016 LEU cc_start: 0.8431 (tp) cc_final: 0.8223 (tt)
REVERT: A 1024 LYS cc_start: 0.8432 (tttt) cc_final: 0.8154 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8513 (tttt) cc_final: 0.8184 (ttmm)
REVERT: A 1133 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8177 (mmtt)
REVERT: A 1136 MET cc_start: 0.6733 (ptt) cc_final: 0.6352 (ptt)
REVERT: A 1148 THR cc_start: 0.8237 (p) cc_final: 0.7983 (t)
REVERT: A 1318 ASP cc_start: 0.7616 (t70) cc_final: 0.7306 (t0)
REVERT: A 1368 ILE cc_start: 0.7805 (mt) cc_final: 0.7587 (mm)
REVERT: A 1373 LYS cc_start: 0.8216 (tttt) cc_final: 0.7875 (tttm)
REVERT: A 1381 ASN cc_start: 0.8362 (m-40) cc_final: 0.8159 (m-40)
REVERT: A 1382 MET cc_start: 0.8661 (mtt) cc_final: 0.8412 (mtm)
REVERT: A 1399 TYR cc_start: 0.8343 (m-80) cc_final: 0.7788 (m-80)
REVERT: A 1565 SER cc_start: 0.8422 (m) cc_final: 0.8191 (p)
REVERT: A 1619 LYS cc_start: 0.8287 (tttt) cc_final: 0.8026 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7685 (ttm-80)
REVERT: A 1640 MET cc_start: 0.7743 (ttp) cc_final: 0.7123 (ttp)
REVERT: A 1647 MET cc_start: 0.8272 (ttp) cc_final: 0.8061 (ttm)
REVERT: A 2298 MET cc_start: 0.7560 (mtp) cc_final: 0.7293 (mtp)
REVERT: A 2301 ARG cc_start: 0.8452 (ttm110) cc_final: 0.8188 (ttm-80)
REVERT: A 2392 THR cc_start: 0.8399 (p) cc_final: 0.8073 (p)
REVERT: A 2395 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8130 (mtmm)
REVERT: A 2479 THR cc_start: 0.7834 (m) cc_final: 0.7324 (p)
REVERT: A 2641 PHE cc_start: 0.7934 (m-80) cc_final: 0.7229 (t80)
REVERT: A 2692 GLN cc_start: 0.8513 (tt0) cc_final: 0.8305 (tt0)
REVERT: A 2746 PHE cc_start: 0.7791 (m-80) cc_final: 0.7581 (m-80)
REVERT: A 2810 LYS cc_start: 0.8560 (mttt) cc_final: 0.8345 (mtmm)
REVERT: A 2818 LEU cc_start: 0.8288 (tt) cc_final: 0.8087 (tp)
REVERT: A 2835 TYR cc_start: 0.8626 (m-80) cc_final: 0.7907 (m-80)
REVERT: A 2861 GLU cc_start: 0.7772 (tt0) cc_final: 0.7465 (tt0)
REVERT: A 2862 ASP cc_start: 0.7546 (t70) cc_final: 0.7264 (t0)
REVERT: A 3016 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7771 (mt-10)
REVERT: A 3109 MET cc_start: 0.7927 (mtt) cc_final: 0.7476 (mtm)
REVERT: A 3139 MET cc_start: 0.7172 (ttt) cc_final: 0.6632 (tmt)
REVERT: A 3151 MET cc_start: 0.7277 (ptt) cc_final: 0.6989 (tmm)
  outliers start: 0
  outliers final: 1
  residues processed: 367
  average time/residue: 0.6918
  time to fit residues: 272.0717
Evaluate side-chains
  304 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 303
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1613 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 944 HIS
A 987 ASN
A1068 ASN
A1277 GLN
A1514 ASN
A1582 GLN
A1613 ASN
A1758 ASN
A2314 ASN
A2334 ASN
A2396 ASN
A2476 HIS
A2560 GLN
A2644 HIS
A2702 GLN
A2857 ASN
A2961 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.153532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.129193 restraints weight = 16217.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 1.96
r_work: 0.3626 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3475 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11994  Z= 0.127
  Angle     :  0.519   7.340  16164  Z= 0.263
  Chirality :  0.039   0.183   1862
  Planarity :  0.004   0.051   2045
  Dihedral  :  4.099  37.962   1589
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.32 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.22), residues: 1447
  helix:  1.07 (0.18), residues: 831
  sheet: -0.10 (0.60), residues: 77
  loop : -1.15 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A3025 
 TYR   0.011   0.001   TYR A2836 
 PHE   0.031   0.001   PHE A2633 
 TRP   0.018   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.13 (11990)
  covalent geometry    : angle       0.51125 /  0.26 (16158)
  hydrogen bonds       : bond        0.03802 /  2.47 (  633)
  hydrogen bonds       : angle       4.40042 /  3.16 ( 1833)
  metal coordination   : bond        0.00523 /  0.30 (    4)
  metal coordination   : angle       4.63510 /  3.09 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 304
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A  939 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7980 (mm-30)
REVERT: A  963 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7546 (ttp80)
REVERT: A 1001 LYS cc_start: 0.8673 (pttt) cc_final: 0.8467 (ptmt)
REVERT: A 1024 LYS cc_start: 0.8424 (tttt) cc_final: 0.8150 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8351 (tttt) cc_final: 0.8072 (ttmm)
REVERT: A 1079 CYS cc_start: 0.8149 (t) cc_final: 0.7877 (m)
REVERT: A 1133 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8231 (mmtt)
REVERT: A 1136 MET cc_start: 0.6640 (ptt) cc_final: 0.6322 (ptt)
REVERT: A 1138 MET cc_start: 0.6348 (mtp) cc_final: 0.5893 (ttm)
REVERT: A 1279 PHE cc_start: 0.8357 (m-80) cc_final: 0.7918 (m-80)
REVERT: A 1318 ASP cc_start: 0.7644 (t70) cc_final: 0.7350 (t0)
REVERT: A 1348 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7212 (ttm-80)
REVERT: A 1373 LYS cc_start: 0.8174 (tttt) cc_final: 0.7864 (tttm)
REVERT: A 1382 MET cc_start: 0.8604 (mtt) cc_final: 0.8393 (mtm)
REVERT: A 1399 TYR cc_start: 0.8321 (m-80) cc_final: 0.8027 (m-80)
REVERT: A 1410 SER cc_start: 0.8400 (m) cc_final: 0.8177 (t)
REVERT: A 1619 LYS cc_start: 0.8360 (tttt) cc_final: 0.8083 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7618 (ttm-80)
REVERT: A 2301 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8119 (ttm-80)
REVERT: A 2395 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8019 (mtmm)
REVERT: A 2481 SER cc_start: 0.8501 (m) cc_final: 0.8150 (t)
REVERT: A 2492 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6928 (tm-30)
REVERT: A 2496 ILE cc_start: 0.8576 (mt) cc_final: 0.8304 (mt)
REVERT: A 2641 PHE cc_start: 0.7880 (m-80) cc_final: 0.7255 (t80)
REVERT: A 2810 LYS cc_start: 0.8563 (mttt) cc_final: 0.8352 (mtmm)
REVERT: A 2835 TYR cc_start: 0.8582 (m-80) cc_final: 0.7994 (m-80)
REVERT: A 2861 GLU cc_start: 0.7748 (tt0) cc_final: 0.7458 (tt0)
REVERT: A 2862 ASP cc_start: 0.7563 (t70) cc_final: 0.7327 (t0)
REVERT: A 3025 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.7096 (mtm-85)
REVERT: A 3109 MET cc_start: 0.7964 (mtt) cc_final: 0.7455 (mpp)
REVERT: A 3151 MET cc_start: 0.7097 (ptt) cc_final: 0.6866 (tmm)
  outliers start: 23
  outliers final: 10
  residues processed: 315
  average time/residue: 0.6894
  time to fit residues: 232.6840
Evaluate side-chains
  284 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 274
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  979 SER
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1798 GLU
Chi-restraints excluded: chain A residue 2699 VAL
Chi-restraints excluded: chain A residue 2703 SER
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 3037 ARG
Chi-restraints excluded: chain A residue 3209 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 127 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 129 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0870
   chunk 119 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A1060 ASN
A1068 ASN
A1277 GLN
A1556 ASN
A2314 ASN
A2323 ASN
A2334 ASN
A2376 GLN
A2477 HIS
** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2695 GLN
A2702 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.153132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.128731 restraints weight = 16236.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 1.97
r_work: 0.3611 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11994  Z= 0.138
  Angle     :  0.511   8.336  16164  Z= 0.260
  Chirality :  0.039   0.150   1862
  Planarity :  0.004   0.047   2045
  Dihedral  :  3.854  23.840   1587
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.63 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.22), residues: 1447
  helix:  1.36 (0.18), residues: 832
  sheet: -0.22 (0.57), residues: 82
  loop : -1.11 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1486 
 TYR   0.012   0.001   TYR A2836 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.007   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 (11990)
  covalent geometry    : angle       0.50505 /  0.26 (16158)
  hydrogen bonds       : bond        0.03629 /  2.36 (  633)
  hydrogen bonds       : angle       4.18703 /  3.01 ( 1833)
  metal coordination   : bond        0.00617 /  0.35 (    4)
  metal coordination   : angle       4.14562 /  2.78 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 288
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
REVERT: A  939 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8078 (mm-30)
REVERT: A  994 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7487 (tm-30)
REVERT: A 1024 LYS cc_start: 0.8417 (tttt) cc_final: 0.8158 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8383 (tttt) cc_final: 0.8104 (ttmm)
REVERT: A 1075 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8312 (p)
REVERT: A 1133 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8072 (mmtt)
REVERT: A 1136 MET cc_start: 0.6586 (ptt) cc_final: 0.6331 (ptt)
REVERT: A 1279 PHE cc_start: 0.8373 (m-80) cc_final: 0.7877 (m-80)
REVERT: A 1318 ASP cc_start: 0.7602 (t70) cc_final: 0.7311 (t0)
REVERT: A 1325 ASN cc_start: 0.8149 (m-40) cc_final: 0.7874 (m110)
REVERT: A 1364 ARG cc_start: 0.7474 (mtt90) cc_final: 0.7252 (mtt90)
REVERT: A 1373 LYS cc_start: 0.8162 (tttt) cc_final: 0.7852 (tttp)
REVERT: A 1382 MET cc_start: 0.8692 (mtt) cc_final: 0.8463 (mtm)
REVERT: A 1399 TYR cc_start: 0.8334 (m-80) cc_final: 0.8025 (m-80)
REVERT: A 1410 SER cc_start: 0.8428 (m) cc_final: 0.8208 (t)
REVERT: A 1619 LYS cc_start: 0.8356 (tttt) cc_final: 0.8114 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7642 (ttm-80)
REVERT: A 2301 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8085 (ttm-80)
REVERT: A 2395 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8072 (mtmm)
REVERT: A 2481 SER cc_start: 0.8538 (m) cc_final: 0.8218 (t)
REVERT: A 2492 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6979 (tm-30)
REVERT: A 2496 ILE cc_start: 0.8673 (mt) cc_final: 0.8298 (mt)
REVERT: A 2578 SER cc_start: 0.8579 (m) cc_final: 0.8233 (p)
REVERT: A 2641 PHE cc_start: 0.7874 (m-80) cc_final: 0.7216 (t80)
REVERT: A 2810 LYS cc_start: 0.8589 (mttt) cc_final: 0.8379 (mtmm)
REVERT: A 2839 PHE cc_start: 0.8252 (m-80) cc_final: 0.7922 (m-80)
REVERT: A 2861 GLU cc_start: 0.7738 (tt0) cc_final: 0.7434 (tt0)
REVERT: A 2862 ASP cc_start: 0.7569 (t0) cc_final: 0.7329 (t0)
REVERT: A 3077 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7774 (mp0)
REVERT: A 3109 MET cc_start: 0.8031 (mtt) cc_final: 0.7543 (mpp)
REVERT: A 3151 MET cc_start: 0.7180 (ptt) cc_final: 0.6886 (tmm)
REVERT: A 3184 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8083 (mtm)
REVERT: A 3203 MET cc_start: 0.6777 (mpp) cc_final: 0.6297 (tpp)
  outliers start: 26
  outliers final: 13
  residues processed: 298
  average time/residue: 0.7019
  time to fit residues: 224.0386
Evaluate side-chains
  287 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 272
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  929 VAL
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  979 SER
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1798 GLU
Chi-restraints excluded: chain A residue 2587 THR
Chi-restraints excluded: chain A residue 2699 VAL
Chi-restraints excluded: chain A residue 2703 SER
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2815 ARG
Chi-restraints excluded: chain A residue 3037 ARG
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3209 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 139 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 110 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 25 optimal weight:    8.9990
   chunk 105 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 119 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A1068 ASN
A1277 GLN
** A1421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 GLN
A1521 GLN
A1540 ASN
A1582 GLN
A2314 ASN
A2323 ASN
A2334 ASN
A2477 HIS
** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2692 GLN
A2695 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.151643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.127046 restraints weight = 16251.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 1.98
r_work: 0.3594 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  11994  Z= 0.158
  Angle     :  0.519   8.569  16164  Z= 0.263
  Chirality :  0.040   0.138   1862
  Planarity :  0.004   0.045   2045
  Dihedral  :  3.875  23.928   1587
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.22 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.22), residues: 1447
  helix:  1.42 (0.18), residues: 841
  sheet: -0.22 (0.56), residues: 82
  loop : -1.06 (0.27), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A3025 
 TYR   0.014   0.001   TYR A1054 
 PHE   0.026   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.008   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.16 (11990)
  covalent geometry    : angle       0.51304 /  0.26 (16158)
  hydrogen bonds       : bond        0.03663 /  2.39 (  633)
  hydrogen bonds       : angle       4.08626 /  2.94 ( 1833)
  metal coordination   : bond        0.00702 /  0.39 (    4)
  metal coordination   : angle       3.97533 /  2.72 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 292
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  939 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8147 (mm-30)
REVERT: A  943 GLU cc_start: 0.7973 (pt0) cc_final: 0.7746 (pt0)
REVERT: A 1024 LYS cc_start: 0.8450 (tttt) cc_final: 0.8186 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8401 (tttt) cc_final: 0.8118 (ttmm)
REVERT: A 1051 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (tp)
REVERT: A 1075 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8376 (p)
REVERT: A 1079 CYS cc_start: 0.8250 (t) cc_final: 0.7982 (m)
REVERT: A 1136 MET cc_start: 0.6464 (ptt) cc_final: 0.6211 (ptt)
REVERT: A 1279 PHE cc_start: 0.8378 (m-80) cc_final: 0.7907 (m-80)
REVERT: A 1318 ASP cc_start: 0.7549 (t70) cc_final: 0.7258 (t0)
REVERT: A 1325 ASN cc_start: 0.8174 (m-40) cc_final: 0.7878 (m110)
REVERT: A 1364 ARG cc_start: 0.7496 (mmt90) cc_final: 0.7241 (mtt90)
REVERT: A 1403 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7509 (ttp80)
REVERT: A 1410 SER cc_start: 0.8422 (m) cc_final: 0.8211 (t)
REVERT: A 1619 LYS cc_start: 0.8362 (tttt) cc_final: 0.8122 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7620 (ttm-80)
REVERT: A 1641 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8028 (mm)
REVERT: A 2301 ARG cc_start: 0.8377 (ttm110) cc_final: 0.8157 (mtt-85)
REVERT: A 2349 PHE cc_start: 0.8366 (t80) cc_final: 0.8133 (t80)
REVERT: A 2395 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8116 (mtmm)
REVERT: A 2481 SER cc_start: 0.8539 (m) cc_final: 0.8225 (t)
REVERT: A 2492 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6981 (tm-30)
REVERT: A 2496 ILE cc_start: 0.8646 (mt) cc_final: 0.8249 (mt)
REVERT: A 2641 PHE cc_start: 0.7900 (m-80) cc_final: 0.7257 (t80)
REVERT: A 2839 PHE cc_start: 0.8334 (m-80) cc_final: 0.7971 (m-80)
REVERT: A 2861 GLU cc_start: 0.7718 (tt0) cc_final: 0.7399 (tt0)
REVERT: A 2862 ASP cc_start: 0.7604 (t0) cc_final: 0.7363 (t0)
REVERT: A 3016 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7653 (mt-10)
REVERT: A 3025 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.7116 (mtm-85)
REVERT: A 3071 VAL cc_start: 0.8530 (t) cc_final: 0.8308 (m)
REVERT: A 3077 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7727 (mp0)
REVERT: A 3109 MET cc_start: 0.8026 (mtt) cc_final: 0.7543 (mpp)
REVERT: A 3135 ARG cc_start: 0.7324 (ttt-90) cc_final: 0.6994 (ttt-90)
REVERT: A 3151 MET cc_start: 0.7219 (ptt) cc_final: 0.6897 (tmm)
REVERT: A 3184 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8091 (mtm)
REVERT: A 3198 LEU cc_start: 0.8566 (mp) cc_final: 0.8333 (mt)
REVERT: A 3203 MET cc_start: 0.6867 (mpp) cc_final: 0.6312 (tpp)
  outliers start: 35
  outliers final: 20
  residues processed: 303
  average time/residue: 0.6748
  time to fit residues: 219.4828
Evaluate side-chains
  303 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 278
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  979 SER
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1390 ASN
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1403 ARG
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1647 MET
Chi-restraints excluded: chain A residue 1798 GLU
Chi-restraints excluded: chain A residue 2587 THR
Chi-restraints excluded: chain A residue 2699 VAL
Chi-restraints excluded: chain A residue 2703 SER
Chi-restraints excluded: chain A residue 2764 SER
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2815 ARG
Chi-restraints excluded: chain A residue 3027 VAL
Chi-restraints excluded: chain A residue 3037 ARG
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3209 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 85 optimal weight:    0.1980
   chunk 104 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 121 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1060 ASN
A1068 ASN
A1277 GLN
** A1421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1582 GLN
A2314 ASN
A2323 ASN
A2334 ASN
A2477 HIS
A2619 GLN
A2692 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.151705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.127091 restraints weight = 16170.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 1.97
r_work: 0.3592 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11994  Z= 0.152
  Angle     :  0.520   8.644  16164  Z= 0.263
  Chirality :  0.039   0.174   1862
  Planarity :  0.004   0.061   2045
  Dihedral  :  3.875  23.999   1587
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.25 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.22), residues: 1447
  helix:  1.63 (0.18), residues: 827
  sheet: -0.20 (0.58), residues: 77
  loop : -1.02 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A3025 
 TYR   0.016   0.001   TYR A1054 
 PHE   0.024   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.009   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 (11990)
  covalent geometry    : angle       0.51474 /  0.26 (16158)
  hydrogen bonds       : bond        0.03588 /  2.33 (  633)
  hydrogen bonds       : angle       4.04685 /  2.91 ( 1833)
  metal coordination   : bond        0.00607 /  0.36 (    4)
  metal coordination   : angle       3.84037 /  2.62 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 275
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  939 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8184 (mm-30)
REVERT: A  943 GLU cc_start: 0.8022 (pt0) cc_final: 0.7750 (pt0)
REVERT: A 1024 LYS cc_start: 0.8467 (tttt) cc_final: 0.8192 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8444 (tttt) cc_final: 0.8148 (ttmm)
REVERT: A 1051 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8197 (tp)
REVERT: A 1075 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8375 (p)
REVERT: A 1079 CYS cc_start: 0.8238 (t) cc_final: 0.7953 (m)
REVERT: A 1133 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8063 (mmtt)
REVERT: A 1277 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7756 (mp10)
REVERT: A 1279 PHE cc_start: 0.8375 (m-80) cc_final: 0.7902 (m-80)
REVERT: A 1318 ASP cc_start: 0.7569 (t70) cc_final: 0.7287 (t0)
REVERT: A 1325 ASN cc_start: 0.8159 (m-40) cc_final: 0.7858 (m110)
REVERT: A 1335 GLU cc_start: 0.8046 (mp0) cc_final: 0.7756 (mp0)
REVERT: A 1403 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7485 (ttp80)
REVERT: A 1612 TYR cc_start: 0.8498 (m-80) cc_final: 0.8242 (m-80)
REVERT: A 1619 LYS cc_start: 0.8363 (tttt) cc_final: 0.8125 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7634 (ttm-80)
REVERT: A 1641 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.8008 (mm)
REVERT: A 2301 ARG cc_start: 0.8363 (ttm110) cc_final: 0.8096 (mtt-85)
REVERT: A 2349 PHE cc_start: 0.8402 (t80) cc_final: 0.8163 (t80)
REVERT: A 2395 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8113 (mtmm)
REVERT: A 2481 SER cc_start: 0.8570 (m) cc_final: 0.8235 (t)
REVERT: A 2492 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7127 (tm-30)
REVERT: A 2641 PHE cc_start: 0.7890 (m-80) cc_final: 0.7253 (t80)
REVERT: A 2839 PHE cc_start: 0.8341 (m-80) cc_final: 0.7966 (m-80)
REVERT: A 2861 GLU cc_start: 0.7694 (tt0) cc_final: 0.7374 (tt0)
REVERT: A 2862 ASP cc_start: 0.7597 (t0) cc_final: 0.7378 (t0)
REVERT: A 3016 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7635 (mt-10)
REVERT: A 3109 MET cc_start: 0.8039 (mtt) cc_final: 0.7551 (mpp)
REVERT: A 3135 ARG cc_start: 0.7336 (ttt-90) cc_final: 0.6986 (ttt-90)
REVERT: A 3151 MET cc_start: 0.7214 (ptt) cc_final: 0.6953 (tmm)
REVERT: A 3184 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7764 (mtm)
REVERT: A 3198 LEU cc_start: 0.8552 (mp) cc_final: 0.8291 (mt)
REVERT: A 3199 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8467 (mtpp)
REVERT: A 3203 MET cc_start: 0.6911 (mpp) cc_final: 0.6307 (tpp)
  outliers start: 40
  outliers final: 26
  residues processed: 292
  average time/residue: 0.6871
  time to fit residues: 215.3530
Evaluate side-chains
  302 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 270
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  929 VAL
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  979 SER
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1277 GLN
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1390 ASN
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1403 ARG
Chi-restraints excluded: chain A residue 1420 ILE
Chi-restraints excluded: chain A residue 1570 VAL
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1647 MET
Chi-restraints excluded: chain A residue 1763 LEU
Chi-restraints excluded: chain A residue 1798 GLU
Chi-restraints excluded: chain A residue 2587 THR
Chi-restraints excluded: chain A residue 2699 VAL
Chi-restraints excluded: chain A residue 2703 SER
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2779 ILE
Chi-restraints excluded: chain A residue 2815 ARG
Chi-restraints excluded: chain A residue 3027 VAL
Chi-restraints excluded: chain A residue 3037 ARG
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3209 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 120 optimal weight:    1.9990
   chunk 117 optimal weight:    0.1980
   chunk 86 optimal weight:    0.0000
   chunk 27 optimal weight:    0.7980
   chunk 25 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A1068 ASN
A1277 GLN
** A1421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1785 GLN
A2314 ASN
A2323 ASN
A2334 ASN
A2477 HIS
A2692 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.152120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.127781 restraints weight = 16179.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.97
r_work: 0.3603 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11994  Z= 0.126
  Angle     :  0.505   8.535  16164  Z= 0.256
  Chirality :  0.039   0.161   1862
  Planarity :  0.004   0.051   2045
  Dihedral  :  3.819  23.843   1587
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.29 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.23), residues: 1447
  helix:  1.76 (0.18), residues: 827
  sheet: -0.25 (0.59), residues: 73
  loop : -0.98 (0.27), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A3025 
 TYR   0.016   0.001   TYR A1054 
 PHE   0.022   0.001   PHE A2370 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.009   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 (11990)
  covalent geometry    : angle       0.50076 /  0.26 (16158)
  hydrogen bonds       : bond        0.03409 /  2.22 (  633)
  hydrogen bonds       : angle       3.97291 /  2.86 ( 1833)
  metal coordination   : bond        0.00508 /  0.29 (    4)
  metal coordination   : angle       3.39919 /  2.35 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 278
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  939 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8128 (mm-30)
REVERT: A  943 GLU cc_start: 0.7998 (pt0) cc_final: 0.7738 (pt0)
REVERT: A 1024 LYS cc_start: 0.8426 (tttt) cc_final: 0.8155 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8399 (tttt) cc_final: 0.8102 (ttmm)
REVERT: A 1051 LEU cc_start: 0.8433 (tp) cc_final: 0.8186 (tp)
REVERT: A 1075 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8418 (p)
REVERT: A 1079 CYS cc_start: 0.8227 (t) cc_final: 0.7778 (m)
REVERT: A 1133 LYS cc_start: 0.8479 (mmtt) cc_final: 0.7948 (mmtt)
REVERT: A 1279 PHE cc_start: 0.8377 (m-80) cc_final: 0.7871 (m-80)
REVERT: A 1318 ASP cc_start: 0.7588 (t70) cc_final: 0.7303 (t0)
REVERT: A 1325 ASN cc_start: 0.8134 (m-40) cc_final: 0.7828 (m110)
REVERT: A 1335 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7718 (mp0)
REVERT: A 1364 ARG cc_start: 0.7535 (mmt90) cc_final: 0.7322 (mtt90)
REVERT: A 1403 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7472 (ttp80)
REVERT: A 1612 TYR cc_start: 0.8490 (m-80) cc_final: 0.8209 (m-80)
REVERT: A 1619 LYS cc_start: 0.8324 (tttt) cc_final: 0.8084 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7597 (ttm-80)
REVERT: A 1641 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7974 (mm)
REVERT: A 2301 ARG cc_start: 0.8325 (ttm110) cc_final: 0.8094 (mtt-85)
REVERT: A 2349 PHE cc_start: 0.8369 (t80) cc_final: 0.8137 (t80)
REVERT: A 2395 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8085 (mtmm)
REVERT: A 2481 SER cc_start: 0.8522 (m) cc_final: 0.8198 (t)
REVERT: A 2492 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6971 (tm-30)
REVERT: A 2496 ILE cc_start: 0.8600 (mt) cc_final: 0.8138 (mt)
REVERT: A 2575 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6675 (tm-30)
REVERT: A 2641 PHE cc_start: 0.7876 (m-80) cc_final: 0.7239 (t80)
REVERT: A 2788 GLU cc_start: 0.7613 (mp0) cc_final: 0.7400 (mm-30)
REVERT: A 2839 PHE cc_start: 0.8340 (m-80) cc_final: 0.7975 (m-80)
REVERT: A 2861 GLU cc_start: 0.7681 (tt0) cc_final: 0.7364 (tt0)
REVERT: A 2862 ASP cc_start: 0.7597 (t0) cc_final: 0.7371 (t0)
REVERT: A 3016 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7631 (mt-10)
REVERT: A 3025 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.7150 (mtm-85)
REVERT: A 3109 MET cc_start: 0.8038 (mtt) cc_final: 0.7621 (mpp)
REVERT: A 3151 MET cc_start: 0.7214 (ptt) cc_final: 0.6947 (tmm)
REVERT: A 3184 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7785 (mtm)
REVERT: A 3198 LEU cc_start: 0.8570 (mp) cc_final: 0.8305 (mt)
REVERT: A 3203 MET cc_start: 0.6904 (mpp) cc_final: 0.6279 (tpp)
  outliers start: 41
  outliers final: 24
  residues processed: 296
  average time/residue: 0.6729
  time to fit residues: 213.6914
Evaluate side-chains
  305 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 275
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  929 VAL
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  979 SER
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1335 GLU
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1403 ARG
Chi-restraints excluded: chain A residue 1570 VAL
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1647 MET
Chi-restraints excluded: chain A residue 1763 LEU
Chi-restraints excluded: chain A residue 1798 GLU
Chi-restraints excluded: chain A residue 2575 GLU
Chi-restraints excluded: chain A residue 2587 THR
Chi-restraints excluded: chain A residue 2703 SER
Chi-restraints excluded: chain A residue 2764 SER
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2779 ILE
Chi-restraints excluded: chain A residue 2815 ARG
Chi-restraints excluded: chain A residue 3026 CYS
Chi-restraints excluded: chain A residue 3027 VAL
Chi-restraints excluded: chain A residue 3037 ARG
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3209 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 142 optimal weight:    0.0370
   chunk 1 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9990
   chunk 139 optimal weight:    0.5980
   chunk 22 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 136 optimal weight:    0.8980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A1060 ASN
A1068 ASN
** A1421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1669 ASN
A2314 ASN
A2323 ASN
A2334 ASN
A2477 HIS
A2692 GLN
A3170 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.151462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.127066 restraints weight = 16107.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.97
r_work: 0.3597 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11994  Z= 0.141
  Angle     :  0.524   8.833  16164  Z= 0.262
  Chirality :  0.039   0.160   1862
  Planarity :  0.004   0.053   2045
  Dihedral  :  3.821  24.042   1587
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.02 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.23), residues: 1447
  helix:  1.81 (0.18), residues: 828
  sheet: -0.17 (0.58), residues: 77
  loop : -1.00 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A3025 
 TYR   0.018   0.001   TYR A1054 
 PHE   0.021   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.011   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 (11990)
  covalent geometry    : angle       0.51946 /  0.26 (16158)
  hydrogen bonds       : bond        0.03485 /  2.26 (  633)
  hydrogen bonds       : angle       3.96388 /  2.85 ( 1833)
  metal coordination   : bond        0.00611 /  0.36 (    4)
  metal coordination   : angle       3.54486 /  2.46 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 275
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  939 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8183 (mm-30)
REVERT: A  943 GLU cc_start: 0.8018 (pt0) cc_final: 0.7751 (pt0)
REVERT: A 1024 LYS cc_start: 0.8461 (tttt) cc_final: 0.8205 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8408 (tttt) cc_final: 0.8096 (ttmm)
REVERT: A 1051 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8203 (tp)
REVERT: A 1075 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8460 (p)
REVERT: A 1112 LEU cc_start: 0.8446 (mt) cc_final: 0.8169 (mt)
REVERT: A 1279 PHE cc_start: 0.8377 (m-80) cc_final: 0.7905 (m-80)
REVERT: A 1318 ASP cc_start: 0.7577 (t70) cc_final: 0.7275 (t0)
REVERT: A 1325 ASN cc_start: 0.8144 (m-40) cc_final: 0.7842 (m110)
REVERT: A 1335 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7680 (mp0)
REVERT: A 1364 ARG cc_start: 0.7527 (mmt90) cc_final: 0.7220 (mtt90)
REVERT: A 1403 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7455 (ttp80)
REVERT: A 1612 TYR cc_start: 0.8506 (m-80) cc_final: 0.8281 (m-80)
REVERT: A 1619 LYS cc_start: 0.8363 (tttt) cc_final: 0.8116 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7612 (ttm-80)
REVERT: A 1641 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7965 (mm)
REVERT: A 2301 ARG cc_start: 0.8342 (ttm110) cc_final: 0.8135 (mtt-85)
REVERT: A 2349 PHE cc_start: 0.8373 (t80) cc_final: 0.8150 (t80)
REVERT: A 2395 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8126 (mtmm)
REVERT: A 2481 SER cc_start: 0.8581 (m) cc_final: 0.8259 (t)
REVERT: A 2492 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7102 (tm-30)
REVERT: A 2575 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6716 (tm-30)
REVERT: A 2578 SER cc_start: 0.8543 (m) cc_final: 0.8214 (p)
REVERT: A 2641 PHE cc_start: 0.7867 (m-80) cc_final: 0.7239 (t80)
REVERT: A 2839 PHE cc_start: 0.8347 (m-80) cc_final: 0.7970 (m-80)
REVERT: A 2861 GLU cc_start: 0.7692 (tt0) cc_final: 0.7377 (tt0)
REVERT: A 2862 ASP cc_start: 0.7570 (t0) cc_final: 0.7359 (t0)
REVERT: A 2864 MET cc_start: 0.7119 (mmt) cc_final: 0.6886 (mmt)
REVERT: A 3016 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7657 (mt-10)
REVERT: A 3109 MET cc_start: 0.8040 (mtt) cc_final: 0.7628 (mpp)
REVERT: A 3151 MET cc_start: 0.7210 (ptt) cc_final: 0.6956 (tmm)
REVERT: A 3184 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7786 (mtm)
REVERT: A 3198 LEU cc_start: 0.8572 (mp) cc_final: 0.8329 (mt)
REVERT: A 3203 MET cc_start: 0.6917 (mpp) cc_final: 0.6298 (tpp)
  outliers start: 36
  outliers final: 23
  residues processed: 289
  average time/residue: 0.7017
  time to fit residues: 217.1443
Evaluate side-chains
  300 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 270
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  929 VAL
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  979 SER
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1335 GLU
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1403 ARG
Chi-restraints excluded: chain A residue 1570 VAL
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1647 MET
Chi-restraints excluded: chain A residue 1763 LEU
Chi-restraints excluded: chain A residue 2496 ILE
Chi-restraints excluded: chain A residue 2575 GLU
Chi-restraints excluded: chain A residue 2703 SER
Chi-restraints excluded: chain A residue 2764 SER
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2805 SER
Chi-restraints excluded: chain A residue 2815 ARG
Chi-restraints excluded: chain A residue 3026 CYS
Chi-restraints excluded: chain A residue 3027 VAL
Chi-restraints excluded: chain A residue 3037 ARG
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3209 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0770
   chunk 88 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 138 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
A1060 ASN
A1068 ASN
A1277 GLN
A1395 GLN
A1421 GLN
A2314 ASN
A2323 ASN
A2334 ASN
** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2692 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.150989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.126451 restraints weight = 16032.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 1.97
r_work: 0.3589 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11994  Z= 0.152
  Angle     :  0.536   8.931  16164  Z= 0.269
  Chirality :  0.039   0.159   1862
  Planarity :  0.004   0.054   2045
  Dihedral  :  3.851  23.999   1587
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.10 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.23), residues: 1447
  helix:  1.76 (0.18), residues: 835
  sheet: -0.20 (0.58), residues: 77
  loop : -1.01 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A3025 
 TYR   0.017   0.001   TYR A1054 
 PHE   0.022   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.012   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 (11990)
  covalent geometry    : angle       0.53144 /  0.27 (16158)
  hydrogen bonds       : bond        0.03537 /  2.30 (  633)
  hydrogen bonds       : angle       3.99490 /  2.87 ( 1833)
  metal coordination   : bond        0.00650 /  0.38 (    4)
  metal coordination   : angle       3.56110 /  2.46 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 282
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  939 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8141 (mm-30)
REVERT: A  943 GLU cc_start: 0.8023 (pt0) cc_final: 0.7760 (pt0)
REVERT: A 1024 LYS cc_start: 0.8462 (tttt) cc_final: 0.8209 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8392 (tttt) cc_final: 0.8083 (ttmm)
REVERT: A 1051 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8212 (tp)
REVERT: A 1075 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8485 (p)
REVERT: A 1112 LEU cc_start: 0.8442 (mt) cc_final: 0.8162 (mt)
REVERT: A 1277 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7725 (mp10)
REVERT: A 1279 PHE cc_start: 0.8390 (m-80) cc_final: 0.7959 (m-80)
REVERT: A 1318 ASP cc_start: 0.7572 (t70) cc_final: 0.7275 (t0)
REVERT: A 1325 ASN cc_start: 0.8146 (m-40) cc_final: 0.7828 (m110)
REVERT: A 1335 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7661 (mp0)
REVERT: A 1364 ARG cc_start: 0.7538 (mmt90) cc_final: 0.7251 (mtt90)
REVERT: A 1403 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7465 (ttp80)
REVERT: A 1612 TYR cc_start: 0.8505 (m-80) cc_final: 0.8297 (m-80)
REVERT: A 1619 LYS cc_start: 0.8362 (tttt) cc_final: 0.8116 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7606 (ttm-80)
REVERT: A 1641 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7932 (mm)
REVERT: A 2301 ARG cc_start: 0.8333 (ttm110) cc_final: 0.8116 (mtt-85)
REVERT: A 2349 PHE cc_start: 0.8360 (t80) cc_final: 0.8120 (t80)
REVERT: A 2395 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8107 (mtmm)
REVERT: A 2481 SER cc_start: 0.8574 (m) cc_final: 0.8241 (t)
REVERT: A 2492 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7103 (tm-30)
REVERT: A 2575 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6698 (tm-30)
REVERT: A 2578 SER cc_start: 0.8564 (m) cc_final: 0.8228 (p)
REVERT: A 2641 PHE cc_start: 0.7859 (m-80) cc_final: 0.7244 (t80)
REVERT: A 2815 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8298 (mtt180)
REVERT: A 2839 PHE cc_start: 0.8333 (m-80) cc_final: 0.7982 (m-80)
REVERT: A 2861 GLU cc_start: 0.7674 (tt0) cc_final: 0.7368 (tt0)
REVERT: A 2862 ASP cc_start: 0.7576 (t0) cc_final: 0.7360 (t0)
REVERT: A 2864 MET cc_start: 0.7154 (mmt) cc_final: 0.6920 (mmt)
REVERT: A 3016 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7652 (mt-10)
REVERT: A 3025 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7156 (mtm-85)
REVERT: A 3071 VAL cc_start: 0.8527 (t) cc_final: 0.8325 (m)
REVERT: A 3109 MET cc_start: 0.8035 (mtt) cc_final: 0.7614 (mpp)
REVERT: A 3151 MET cc_start: 0.7183 (ptt) cc_final: 0.6855 (tmm)
REVERT: A 3152 LEU cc_start: 0.5700 (tp) cc_final: 0.5203 (tp)
REVERT: A 3184 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7801 (mtm)
REVERT: A 3198 LEU cc_start: 0.8584 (mp) cc_final: 0.8345 (mt)
REVERT: A 3203 MET cc_start: 0.6859 (mpp) cc_final: 0.6163 (tpp)
  outliers start: 40
  outliers final: 23
  residues processed: 299
  average time/residue: 0.6927
  time to fit residues: 222.2765
Evaluate side-chains
  308 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 276
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  979 SER
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1277 GLN
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1335 GLU
Chi-restraints excluded: chain A residue 1390 ASN
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1403 ARG
Chi-restraints excluded: chain A residue 1570 VAL
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1647 MET
Chi-restraints excluded: chain A residue 1763 LEU
Chi-restraints excluded: chain A residue 2496 ILE
Chi-restraints excluded: chain A residue 2575 GLU
Chi-restraints excluded: chain A residue 2699 VAL
Chi-restraints excluded: chain A residue 2703 SER
Chi-restraints excluded: chain A residue 2764 SER
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2805 SER
Chi-restraints excluded: chain A residue 2815 ARG
Chi-restraints excluded: chain A residue 3026 CYS
Chi-restraints excluded: chain A residue 3027 VAL
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3209 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 141 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A1060 ASN
A1068 ASN
A1277 GLN
A1395 GLN
A2314 ASN
A2334 ASN
A3023 ASN
A3103 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.148716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.124410 restraints weight = 16023.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 1.94
r_work: 0.3561 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  11994  Z= 0.251
  Angle     :  0.618  11.424  16164  Z= 0.308
  Chirality :  0.043   0.162   1862
  Planarity :  0.004   0.057   2045
  Dihedral  :  4.075  24.322   1587
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.95 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.23), residues: 1447
  helix:  1.53 (0.18), residues: 840
  sheet: -0.36 (0.57), residues: 82
  loop : -1.07 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1348 
 TYR   0.022   0.002   TYR A1054 
 PHE   0.035   0.002   PHE A2370 
 TRP   0.015   0.002   TRP A2542 
 HIS   0.014   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00588 /  0.25 (11990)
  covalent geometry    : angle       0.61253 /  0.31 (16158)
  hydrogen bonds       : bond        0.04149 /  2.69 (  633)
  hydrogen bonds       : angle       4.18507 /  3.00 ( 1833)
  metal coordination   : bond        0.01119 /  0.64 (    4)
  metal coordination   : angle       4.21597 /  2.84 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 282
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  939 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8245 (mm-30)
REVERT: A  943 GLU cc_start: 0.8034 (pt0) cc_final: 0.7763 (pt0)
REVERT: A  946 LEU cc_start: 0.8465 (mm) cc_final: 0.8255 (mp)
REVERT: A 1024 LYS cc_start: 0.8521 (tttt) cc_final: 0.8274 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8392 (tttt) cc_final: 0.8079 (ttmm)
REVERT: A 1051 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8251 (tp)
REVERT: A 1112 LEU cc_start: 0.8489 (mt) cc_final: 0.8215 (mt)
REVERT: A 1277 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7898 (mp-120)
REVERT: A 1318 ASP cc_start: 0.7613 (t70) cc_final: 0.7325 (t0)
REVERT: A 1325 ASN cc_start: 0.8164 (m-40) cc_final: 0.7865 (m110)
REVERT: A 1335 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7763 (mp0)
REVERT: A 1403 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7485 (ttp80)
REVERT: A 1529 MET cc_start: 0.8747 (mtm) cc_final: 0.8533 (mtp)
REVERT: A 1619 LYS cc_start: 0.8441 (tttt) cc_final: 0.8192 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7687 (ttm-80)
REVERT: A 2301 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8102 (mtt-85)
REVERT: A 2349 PHE cc_start: 0.8398 (t80) cc_final: 0.8172 (t80)
REVERT: A 2395 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8226 (mtmm)
REVERT: A 2480 SER cc_start: 0.8392 (m) cc_final: 0.8081 (p)
REVERT: A 2481 SER cc_start: 0.8608 (m) cc_final: 0.8306 (t)
REVERT: A 2492 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6922 (tm-30)
REVERT: A 2496 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8135 (mt)
REVERT: A 2575 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6755 (tm-30)
REVERT: A 2578 SER cc_start: 0.8614 (m) cc_final: 0.8264 (p)
REVERT: A 2641 PHE cc_start: 0.7902 (m-80) cc_final: 0.7250 (t80)
REVERT: A 2839 PHE cc_start: 0.8376 (m-80) cc_final: 0.8021 (m-80)
REVERT: A 2861 GLU cc_start: 0.7655 (tt0) cc_final: 0.7337 (tt0)
REVERT: A 2862 ASP cc_start: 0.7603 (t0) cc_final: 0.7396 (t0)
REVERT: A 2864 MET cc_start: 0.7212 (mmt) cc_final: 0.7002 (mmt)
REVERT: A 3016 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7679 (mt-10)
REVERT: A 3081 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6491 (mm-30)
REVERT: A 3109 MET cc_start: 0.8048 (mtt) cc_final: 0.7623 (mpp)
REVERT: A 3151 MET cc_start: 0.7308 (ptt) cc_final: 0.6898 (tmm)
REVERT: A 3152 LEU cc_start: 0.5704 (tp) cc_final: 0.5209 (tp)
REVERT: A 3184 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7791 (mtm)
REVERT: A 3198 LEU cc_start: 0.8627 (mp) cc_final: 0.8386 (mt)
REVERT: A 3203 MET cc_start: 0.6925 (mpp) cc_final: 0.6208 (tpp)
  outliers start: 40
  outliers final: 20
  residues processed: 297
  average time/residue: 0.7020
  time to fit residues: 223.5760
Evaluate side-chains
  300 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 273
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  979 SER
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1277 GLN
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1335 GLU
Chi-restraints excluded: chain A residue 1390 ASN
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1403 ARG
Chi-restraints excluded: chain A residue 1570 VAL
Chi-restraints excluded: chain A residue 1647 MET
Chi-restraints excluded: chain A residue 1763 LEU
Chi-restraints excluded: chain A residue 2496 ILE
Chi-restraints excluded: chain A residue 2575 GLU
Chi-restraints excluded: chain A residue 2699 VAL
Chi-restraints excluded: chain A residue 2703 SER
Chi-restraints excluded: chain A residue 2764 SER
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2805 SER
Chi-restraints excluded: chain A residue 2815 ARG
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3209 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 83 optimal weight:    0.4980
   chunk 122 optimal weight:    0.9990
   chunk 145 optimal weight:    0.9990
   chunk 105 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0970
   chunk 59 optimal weight:    0.8980
   chunk 112 optimal weight:    0.7980
   chunk 110 optimal weight:    0.7980
   chunk 146 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A1068 ASN
A1277 GLN
A2323 ASN
A2334 ASN
** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.151863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.127480 restraints weight = 16149.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.97
r_work: 0.3603 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11994  Z= 0.122
  Angle     :  0.541  10.586  16164  Z= 0.270
  Chirality :  0.039   0.154   1862
  Planarity :  0.004   0.058   2045
  Dihedral  :  3.918  24.297   1587
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.42 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.23), residues: 1447
  helix:  1.76 (0.18), residues: 829
  sheet: -0.30 (0.57), residues: 77
  loop : -1.00 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A3025 
 TYR   0.017   0.001   TYR A1054 
 PHE   0.020   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.009   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 (11990)
  covalent geometry    : angle       0.53691 /  0.27 (16158)
  hydrogen bonds       : bond        0.03351 /  2.18 (  633)
  hydrogen bonds       : angle       3.99620 /  2.87 ( 1833)
  metal coordination   : bond        0.00547 /  0.31 (    4)
  metal coordination   : angle       3.31416 /  2.23 (    6)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 275
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  939 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8198 (mm-30)
REVERT: A  943 GLU cc_start: 0.7999 (pt0) cc_final: 0.7742 (pt0)
REVERT: A  946 LEU cc_start: 0.8419 (mm) cc_final: 0.8193 (mp)
REVERT: A  963 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7461 (ttp80)
REVERT: A 1024 LYS cc_start: 0.8471 (tttt) cc_final: 0.8206 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8370 (tttt) cc_final: 0.8072 (ttmm)
REVERT: A 1051 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8217 (tp)
REVERT: A 1112 LEU cc_start: 0.8456 (mt) cc_final: 0.8181 (mt)
REVERT: A 1279 PHE cc_start: 0.8398 (m-80) cc_final: 0.7928 (m-80)
REVERT: A 1318 ASP cc_start: 0.7561 (t70) cc_final: 0.7265 (t0)
REVERT: A 1325 ASN cc_start: 0.8143 (m-40) cc_final: 0.7836 (m110)
REVERT: A 1335 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7663 (mp0)
REVERT: A 1364 ARG cc_start: 0.7548 (mmt90) cc_final: 0.7295 (mtt90)
REVERT: A 1578 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7945 (ttpp)
REVERT: A 1619 LYS cc_start: 0.8349 (tttt) cc_final: 0.8106 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7628 (ttm-80)
REVERT: A 1644 LEU cc_start: 0.8146 (mt) cc_final: 0.7908 (mp)
REVERT: A 2301 ARG cc_start: 0.8327 (ttm110) cc_final: 0.8079 (mtt90)
REVERT: A 2349 PHE cc_start: 0.8326 (t80) cc_final: 0.8073 (t80)
REVERT: A 2395 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8133 (mtmm)
REVERT: A 2481 SER cc_start: 0.8482 (m) cc_final: 0.8105 (p)
REVERT: A 2492 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7115 (tm-30)
REVERT: A 2575 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6571 (tm-30)
REVERT: A 2578 SER cc_start: 0.8540 (m) cc_final: 0.8194 (p)
REVERT: A 2641 PHE cc_start: 0.7831 (m-80) cc_final: 0.7250 (t80)
REVERT: A 2839 PHE cc_start: 0.8308 (m-80) cc_final: 0.7939 (m-80)
REVERT: A 2861 GLU cc_start: 0.7637 (tt0) cc_final: 0.7336 (tt0)
REVERT: A 2864 MET cc_start: 0.7202 (mmt) cc_final: 0.6995 (mmt)
REVERT: A 3016 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7610 (mt-10)
REVERT: A 3081 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6415 (mm-30)
REVERT: A 3109 MET cc_start: 0.8021 (mtt) cc_final: 0.7600 (mpp)
REVERT: A 3151 MET cc_start: 0.7208 (ptt) cc_final: 0.6839 (tmm)
REVERT: A 3152 LEU cc_start: 0.5692 (tp) cc_final: 0.5200 (tp)
REVERT: A 3184 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7774 (mtm)
REVERT: A 3198 LEU cc_start: 0.8584 (mp) cc_final: 0.8338 (mt)
REVERT: A 3203 MET cc_start: 0.6855 (mpp) cc_final: 0.6520 (tpp)
  outliers start: 24
  outliers final: 17
  residues processed: 285
  average time/residue: 0.7072
  time to fit residues: 215.9381
Evaluate side-chains
  292 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 271
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1335 GLU
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1570 VAL
Chi-restraints excluded: chain A residue 1647 MET
Chi-restraints excluded: chain A residue 2496 ILE
Chi-restraints excluded: chain A residue 2575 GLU
Chi-restraints excluded: chain A residue 2699 VAL
Chi-restraints excluded: chain A residue 2764 SER
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2805 SER
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3209 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 140 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 144 optimal weight:    0.3980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A1060 ASN
A1068 ASN
A1284 ASN
A1799 ASN
A2314 ASN
A2334 ASN
** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.150549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.126235 restraints weight = 16198.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 1.96
r_work: 0.3583 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11994  Z= 0.165
  Angle     :  0.571  10.105  16164  Z= 0.286
  Chirality :  0.040   0.156   1862
  Planarity :  0.004   0.059   2045
  Dihedral  :  3.941  24.444   1587
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.01 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.23), residues: 1447
  helix:  1.68 (0.18), residues: 837
  sheet: -0.33 (0.58), residues: 77
  loop : -1.02 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A3025 
 TYR   0.019   0.001   TYR A1054 
 PHE   0.029   0.001   PHE A2370 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.014   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.17 (11990)
  covalent geometry    : angle       0.56675 /  0.29 (16158)
  hydrogen bonds       : bond        0.03628 /  2.35 (  633)
  hydrogen bonds       : angle       4.03100 /  2.89 ( 1833)
  metal coordination   : bond        0.00722 /  0.42 (    4)
  metal coordination   : angle       3.71123 /  2.56 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5659.45 seconds
wall clock time: 97 minutes 11.38 seconds (5831.38 seconds total)