Starting phenix.real_space_refine
on Sun Apr  7 02:09:47 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/04_2024/7qks_14050_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/04_2024/7qks_14050.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/04_2024/7qks_14050.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/04_2024/7qks_14050.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/04_2024/7qks_14050_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/04_2024/7qks_14050_updated.pdb"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    6011      2.51       5
     N    1541      2.21       5
     O    1740      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  790": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1263": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 9339
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1200, 9339
          Unusual residues: {'9Z9': 1}
          Classifications: {'peptide': 1199, 'undetermined': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 1171, None: 1}
            Not linked:
              pdbres="ALA A1288 "
              pdbres="9Z9 A1301 "
          Chain breaks: 2
  Time building chain proxies: 5.44, per 1000 atoms: 0.58
  Number of scatterers: 9339
  At special positions: 0
  Unit cell: (132.246, 105.462, 102.114, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1740      8.00
     N    1541      7.00
     C    6011      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  - 3.50
        Amino acid           : False - 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: 3.62
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2220

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      65.6% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 41
    Processing helix  chain 'A' and resid 52 through 58
      removed outlier: 4.054A  pdb=" N   MET A  58 " --> pdb=" O   ASP A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 79
      removed outlier: 3.740A  pdb=" N   CYS A  65 " --> pdb=" O   TRP A  62 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A  66 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 99
    Processing helix  chain 'A' and resid 105 through 158
      removed outlier: 3.592A  pdb=" N   HIS A 158 " --> pdb=" O   TRP A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 167
    Processing helix  chain 'A' and resid 170 through 177
    Processing helix  chain 'A' and resid 180 through 187
    Processing helix  chain 'A' and resid 189 through 211
    Processing helix  chain 'A' and resid 213 through 260
      removed outlier: 3.830A  pdb=" N   SER A 230 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   THR A 231 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
      Proline residue:  A 232  - end of helix
    Processing helix  chain 'A' and resid 262 through 268
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.682A  pdb=" N   PHE A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 325
      removed outlier: 3.648A  pdb=" N   LYS A 291 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE A 308 " --> pdb=" O   TRP A 304 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   SER A 324 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 344
    Processing helix  chain 'A' and resid 346 through 371
      removed outlier: 3.524A  pdb=" N   ILE A 351 " --> pdb=" O   GLY A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 441
      removed outlier: 3.550A  pdb=" N   ILE A 438 " --> pdb=" O   SER A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 464 through 470
    Processing helix  chain 'A' and resid 485 through 493
      removed outlier: 4.383A  pdb=" N   GLY A 492 " --> pdb=" O   ASN A 488 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   LEU A 493 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 516
    Processing helix  chain 'A' and resid 520 through 523
      No H-bonds generated for 'chain 'A' and resid 520 through 523'
    Processing helix  chain 'A' and resid 543 through 557
      removed outlier: 4.406A  pdb=" N   SER A 557 " --> pdb=" O   ARG A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 587
      removed outlier: 4.226A  pdb=" N   GLY A 577 " --> pdb=" O   THR A 573 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   ILE A 578 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 579 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 602
    Processing helix  chain 'A' and resid 622 through 626
    Processing helix  chain 'A' and resid 631 through 644
    Processing helix  chain 'A' and resid 699 through 705
    Processing helix  chain 'A' and resid 707 through 740
      removed outlier: 4.297A  pdb=" N   TYR A 711 " --> pdb=" O   GLY A 708 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   ILE A 714 " --> pdb=" O   TYR A 711 " (cutoff:3.500A)
      Proline residue:  A 715  - end of helix
      removed outlier: 4.120A  pdb=" N   GLY A 726 " --> pdb=" O   ALA A 723 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   PHE A 727 " --> pdb=" O   GLY A 724 " (cutoff:3.500A)
      Proline residue:  A 728  - end of helix
      removed outlier: 4.465A  pdb=" N   ALA A 731 " --> pdb=" O   PRO A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 800
      removed outlier: 3.533A  pdb=" N   PHE A 749 " --> pdb=" O   PRO A 746 " (cutoff:3.500A)
      Proline residue:  A 750  - end of helix
      removed outlier: 3.855A  pdb=" N   GLY A 761 " --> pdb=" O   LYS A 758 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LEU A 770 " --> pdb=" O   GLY A 767 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   THR A 778 " --> pdb=" O   LEU A 775 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ARG A 795 " --> pdb=" O   MET A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 808
      No H-bonds generated for 'chain 'A' and resid 805 through 808'
    Processing helix  chain 'A' and resid 811 through 813
      No H-bonds generated for 'chain 'A' and resid 811 through 813'
    Processing helix  chain 'A' and resid 815 through 832
      Proline residue:  A 826  - end of helix
      removed outlier: 4.703A  pdb=" N   GLU A 830 " --> pdb=" O   PRO A 826 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   GLY A 831 " --> pdb=" O   GLN A 827 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   LEU A 832 " --> pdb=" O   ASP A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 857
    Processing helix  chain 'A' and resid 859 through 893
      removed outlier: 4.125A  pdb=" N   VAL A 864 " --> pdb=" O   ARG A 860 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR A 866 " --> pdb=" O   GLY A 862 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR A 868 " --> pdb=" O   VAL A 864 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL A 869 " --> pdb=" O   CYS A 865 " (cutoff:3.500A)
      Proline residue:  A 870  - end of helix
      removed outlier: 3.861A  pdb=" N   VAL A 880 " --> pdb=" O   GLY A 876 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE A 890 " --> pdb=" O   PHE A 886 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LEU A 891 " --> pdb=" O   GLU A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 906
    Processing helix  chain 'A' and resid 908 through 913
    Processing helix  chain 'A' and resid 917 through 970
      removed outlier: 3.615A  pdb=" N   LYS A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ARG A 937 " --> pdb=" O   LYS A 933 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   SER A 938 " --> pdb=" O   ARG A 934 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU A 944 " --> pdb=" O   SER A 940 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU A 945 " --> pdb=" O   ARG A 941 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   ASN A 953 " --> pdb=" O   ILE A 949 " (cutoff:3.500A)
      Proline residue:  A 954  - end of helix
    Processing helix  chain 'A' and resid 975 through 994
      removed outlier: 4.036A  pdb=" N   GLU A 994 " --> pdb=" O   GLN A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1017
      Proline residue:  A1000  - end of helix
      removed outlier: 3.526A  pdb=" N   GLY A1003 " --> pdb=" O   PRO A1000 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ALA A1005 " --> pdb=" O   MET A1002 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   ALA A1008 " --> pdb=" O   ALA A1005 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A1016 " --> pdb=" O   ARG A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1052 through 1054
      No H-bonds generated for 'chain 'A' and resid 1052 through 1054'
    Processing helix  chain 'A' and resid 1083 through 1090
      removed outlier: 3.517A  pdb=" N   VAL A1087 " --> pdb=" O   SER A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1108 through 1110
      No H-bonds generated for 'chain 'A' and resid 1108 through 1110'
    Processing helix  chain 'A' and resid 1113 through 1119
    Processing helix  chain 'A' and resid 1134 through 1141
      removed outlier: 4.528A  pdb=" N   GLY A1141 " --> pdb=" O   ASN A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1153 through 1161
    Processing helix  chain 'A' and resid 1165 through 1170
    Processing helix  chain 'A' and resid 1188 through 1201
    Processing helix  chain 'A' and resid 1218 through 1231
      removed outlier: 3.764A  pdb=" N   MET A1222 " --> pdb=" O   SER A1218 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   VAL A1223 " --> pdb=" O   GLU A1219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1267 through 1273
    Processing helix  chain 'A' and resid 1276 through 1287
    Processing sheet with id=  A, first strand: chain 'A' and resid 416 through 418
    Processing sheet with id=  B, first strand: chain 'A' and resid 615 through 620
      removed outlier: 7.235A  pdb=" N   VAL A 610 " --> pdb=" O   VAL A 617 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   THR A 619 " --> pdb=" O   ILE A 608 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ILE A 608 " --> pdb=" O   THR A 619 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   THR A 592 " --> pdb=" O   ILE A 424 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   LEU A 426 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   VAL A 594 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 1065 through 1067
    Processing sheet with id=  D, first strand: chain 'A' and resid 1260 through 1265
      removed outlier: 6.659A  pdb=" N   VAL A1255 " --> pdb=" O   VAL A1262 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   SER A1264 " --> pdb=" O   ILE A1253 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ILE A1253 " --> pdb=" O   SER A1264 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   VAL A1252 " --> pdb=" O   TYR A1072 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   THR A1237 " --> pdb=" O   VAL A1073 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   LEU A1075 " --> pdb=" O   THR A1237 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   THR A1239 " --> pdb=" O   LEU A1075 " (cutoff:3.500A)
      removed outlier: 8.188A  pdb=" N   GLY A1077 " --> pdb=" O   THR A1239 " (cutoff:3.500A)

    567 hydrogen bonds defined for protein.
    1329 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: 2.94

  Time building geometry restraints manager: 3.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2087
        1.33 -     1.45: 1923
        1.45 -     1.57: 5412
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 9500
  Sorted by residual:
  bond pdb=" N   VAL A1076 "
       pdb=" CA  VAL A1076 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.035 1.11e-02 8.12e+03 9.76e+00
  bond pdb=" C   ARG A 405 "
       pdb=" N   PRO A 406 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.026 8.40e-03 1.42e+04 9.45e+00
  bond pdb=" N   ILE A 346 "
       pdb=" CA  ILE A 346 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.037 1.19e-02 7.06e+03 9.44e+00
  bond pdb=" N   ILE A 722 "
       pdb=" CA  ILE A 722 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.19e-02 7.06e+03 9.44e+00
  bond pdb=" N   ILE A 176 "
       pdb=" CA  ILE A 176 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.19e-02 7.06e+03 8.99e+00
  ... (remaining 9495 not shown)

  Histogram of bond angle deviations from ideal:
       99.63 -   106.55: 171
      106.55 -   113.46: 5309
      113.46 -   120.38: 3824
      120.38 -   127.30: 3500
      127.30 -   134.21: 53
  Bond angle restraints: 12857
  Sorted by residual:
  angle pdb=" N   LYS A 354 "
        pdb=" CA  LYS A 354 "
        pdb=" C   LYS A 354 "
      ideal   model   delta    sigma   weight residual
     111.07  106.92    4.15 1.07e+00 8.73e-01 1.50e+01
  angle pdb=" N   GLY A1174 "
        pdb=" CA  GLY A1174 "
        pdb=" C   GLY A1174 "
      ideal   model   delta    sigma   weight residual
     113.18  104.15    9.03 2.37e+00 1.78e-01 1.45e+01
  angle pdb=" CA  GLY A 170 "
        pdb=" C   GLY A 170 "
        pdb=" O   GLY A 170 "
      ideal   model   delta    sigma   weight residual
     120.45  116.61    3.84 1.02e+00 9.61e-01 1.41e+01
  angle pdb=" N   ASP A 179 "
        pdb=" CA  ASP A 179 "
        pdb=" C   ASP A 179 "
      ideal   model   delta    sigma   weight residual
     113.72  109.00    4.72 1.30e+00 5.92e-01 1.32e+01
  angle pdb=" N   ILE A 523 "
        pdb=" CA  ILE A 523 "
        pdb=" C   ILE A 523 "
      ideal   model   delta    sigma   weight residual
     111.45  108.09    3.36 9.30e-01 1.16e+00 1.31e+01
  ... (remaining 12852 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.27: 5434
       24.27 -    48.55: 294
       48.55 -    72.82: 31
       72.82 -    97.09: 6
       97.09 -   121.37: 4
  Dihedral angle restraints: 5769
    sinusoidal: 2307
      harmonic: 3462
  Sorted by residual:
  dihedral pdb=" C21 9Z9 A1301 "
           pdb=" C22 9Z9 A1301 "
           pdb=" C23 9Z9 A1301 "
           pdb=" C24 9Z9 A1301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      77.99  -43.38  121.37     1      3.00e+01 1.11e-03 1.62e+01
  dihedral pdb=" C   PHE A 987 "
           pdb=" N   PHE A 987 "
           pdb=" CA  PHE A 987 "
           pdb=" CB  PHE A 987 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.39    9.79     0      2.50e+00 1.60e-01 1.53e+01
  dihedral pdb=" C18 9Z9 A1301 "
           pdb=" C17 9Z9 A1301 "
           pdb=" O20 9Z9 A1301 "
           pdb=" C21 9Z9 A1301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     163.81  -92.29 -103.90     1      3.00e+01 1.11e-03 1.32e+01
  ... (remaining 5766 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1254
       0.059 -    0.118: 212
       0.118 -    0.177: 31
       0.177 -    0.236: 15
       0.236 -    0.295: 2
  Chirality restraints: 1514
  Sorted by residual:
  chirality pdb=" CA  PHE A 987 "
            pdb=" N   PHE A 987 "
            pdb=" C   PHE A 987 "
            pdb=" CB  PHE A 987 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CA  LEU A1075 "
            pdb=" N   LEU A1075 "
            pdb=" C   LEU A1075 "
            pdb=" CB  LEU A1075 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  ASN A 706 "
            pdb=" N   ASN A 706 "
            pdb=" C   ASN A 706 "
            pdb=" CB  ASN A 706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1511 not shown)

  Planarity restraints: 1608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1092 "   -0.256 9.50e-02 1.11e+02   1.15e-01 8.06e+00
        pdb=" NE  ARG A1092 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1092 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1092 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1092 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 344 "    0.013 2.00e-02 2.50e+03   2.65e-02 7.02e+00
        pdb=" C   LEU A 344 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   LEU A 344 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ILE A 345 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 372 "   -0.232 9.50e-02 1.11e+02   1.04e-01 6.67e+00
        pdb=" NE  ARG A 372 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 372 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 372 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 372 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1605 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 981
        2.75 -     3.29: 9503
        3.29 -     3.82: 15161
        3.82 -     4.36: 18606
        4.36 -     4.90: 32422
  Nonbonded interactions: 76673
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 142 "
            pdb=" NH2 ARG A 889 "
     model   vdw
     2.210 2.520
  nonbonded pdb=" O   GLY A 862 "
            pdb=" OG1 THR A 866 "
     model   vdw
     2.221 2.440
  nonbonded pdb=" O   ILE A1090 "
            pdb=" OH  TYR A1116 "
     model   vdw
     2.228 2.440
  nonbonded pdb=" O   VAL A 939 "
            pdb=" OG1 THR A 943 "
     model   vdw
     2.317 2.440
  nonbonded pdb=" O   LYS A 909 "
            pdb=" OG  SER A 913 "
     model   vdw
     2.346 2.440
  ... (remaining 76668 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:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          5.330
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     28.700
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
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      :  0.005   0.039   9500  Z= 0.334
  Angle     :  0.738   9.091  12857  Z= 0.506
  Chirality :  0.050   0.295   1514
  Planarity :  0.007   0.115   1608
  Dihedral  : 14.589 121.366   3549
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.24), residues: 1193
  helix:  1.06 (0.18), residues: 779
  sheet: -1.59 (0.78), residues: 48
  loop : -0.50 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 955 
 HIS   0.004   0.001   HIS A 103 
 PHE   0.021   0.001   PHE A 119 
 TYR   0.025   0.001   TYR A 248 
 ARG   0.006   0.001   ARG A1019 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7896 (m-30) cc_final: 0.7452 (m-30)
REVERT: A 1248 GLN cc_start: 0.8532 (tt0) cc_final: 0.8294 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 118
  average time/residue: 0.2490
  time to fit residues: 40.9604
Evaluate side-chains
  95 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0870
   chunk 94 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    1.5964

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN
A 633 HIS
A 637 GLN
A1242 HIS
A1248 GLN
A1267 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   9500  Z= 0.303
  Angle     :  0.531  10.340  12857  Z= 0.283
  Chirality :  0.039   0.139   1514
  Planarity :  0.006   0.055   1608
  Dihedral  :  6.349 108.234   1395
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  7.72 %
    Favored  : 91.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.24), residues: 1193
  helix:  1.01 (0.18), residues: 780
  sheet: -1.55 (0.77), residues: 48
  loop : -0.32 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 316 
 HIS   0.007   0.001   HIS A 103 
 PHE   0.017   0.002   PHE A 979 
 TYR   0.026   0.001   TYR A 248 
 ARG   0.006   0.000   ARG A1274 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.041 
Fit side-chains
REVERT: A  369 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8132 (mtt)
REVERT: A 1046 ASP cc_start: 0.7872 (t70) cc_final: 0.7402 (t0)
REVERT: A 1168 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7930 (mp)
REVERT: A 1248 GLN cc_start: 0.8604 (tt0) cc_final: 0.8267 (tp40)
  outliers start: 12
  outliers final: 9
  residues processed: 116
  average time/residue: 0.2470
  time to fit residues: 40.1302
Evaluate side-chains
  107 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1086 THR
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1201 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 109 optimal weight:    0.4980
   chunk 117 optimal weight:    6.9990
   chunk 97 optimal weight:    8.9990
   chunk 108 optimal weight:    0.0770
   chunk 37 optimal weight:    0.0020
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.4746

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

Flipped N/Q/H residues before XYZ refinement:
A1242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9500  Z= 0.138
  Angle     :  0.436   8.923  12857  Z= 0.232
  Chirality :  0.036   0.135   1514
  Planarity :  0.004   0.044   1608
  Dihedral  :  5.805  99.560   1391
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.09 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1193
  helix:  1.23 (0.19), residues: 769
  sheet: -1.44 (0.77), residues: 48
  loop : -0.17 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 213 
 HIS   0.004   0.001   HIS A 103 
 PHE   0.018   0.001   PHE A1167 
 TYR   0.020   0.001   TYR A 248 
 ARG   0.004   0.000   ARG A1050 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 1.091 
Fit side-chains
REVERT: A  165 ASP cc_start: 0.7915 (m-30) cc_final: 0.7708 (m-30)
REVERT: A 1046 ASP cc_start: 0.7799 (t70) cc_final: 0.7266 (t0)
REVERT: A 1168 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7863 (mp)
REVERT: A 1248 GLN cc_start: 0.8626 (tt0) cc_final: 0.8291 (tp40)
  outliers start: 10
  outliers final: 7
  residues processed: 115
  average time/residue: 0.2376
  time to fit residues: 37.6280
Evaluate side-chains
  109 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1201 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0670
   chunk 73 optimal weight:    2.9990
   chunk 109 optimal weight:   20.0000
   chunk 115 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A1242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9500  Z= 0.165
  Angle     :  0.442   9.016  12857  Z= 0.231
  Chirality :  0.036   0.133   1514
  Planarity :  0.004   0.039   1608
  Dihedral  :  5.519  91.274   1391
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 10.68 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.25), residues: 1193
  helix:  1.26 (0.19), residues: 772
  sheet: -1.36 (0.75), residues: 48
  loop :  0.03 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 213 
 HIS   0.005   0.001   HIS A 103 
 PHE   0.017   0.001   PHE A1167 
 TYR   0.024   0.001   TYR A 248 
 ARG   0.008   0.000   ARG A1274 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A 1046 ASP cc_start: 0.7778 (t70) cc_final: 0.7205 (t0)
REVERT: A 1168 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7810 (mp)
REVERT: A 1248 GLN cc_start: 0.8628 (tt0) cc_final: 0.8285 (tp40)
  outliers start: 17
  outliers final: 9
  residues processed: 123
  average time/residue: 0.2370
  time to fit residues: 41.0559
Evaluate side-chains
  113 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1201 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 65 optimal weight:    0.2980
   chunk 1 optimal weight:    0.0270
   chunk 86 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0000
   chunk 98 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0070
   chunk 29 optimal weight:    0.0770
   overall best weight:    0.0818

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9500  Z= 0.109
  Angle     :  0.428   9.628  12857  Z= 0.220
  Chirality :  0.035   0.141   1514
  Planarity :  0.004   0.030   1608
  Dihedral  :  4.981  74.772   1391
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 12.46 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1193
  helix:  1.47 (0.19), residues: 766
  sheet: -0.94 (0.65), residues: 58
  loop :  0.03 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 213 
 HIS   0.002   0.001   HIS A 103 
 PHE   0.006   0.001   PHE A  88 
 TYR   0.011   0.001   TYR A 163 
 ARG   0.006   0.000   ARG A1274 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 1.123 
Fit side-chains
REVERT: A 1046 ASP cc_start: 0.7706 (t70) cc_final: 0.7120 (t0)
REVERT: A 1248 GLN cc_start: 0.8594 (tt0) cc_final: 0.8246 (tp40)
REVERT: A 1267 HIS cc_start: 0.7645 (t70) cc_final: 0.7013 (t70)
  outliers start: 8
  outliers final: 5
  residues processed: 118
  average time/residue: 0.2230
  time to fit residues: 36.8644
Evaluate side-chains
  113 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue 1185 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    0.0270
   chunk 104 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 116 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.8642

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

Flipped N/Q/H residues before XYZ refinement:
** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9500  Z= 0.185
  Angle     :  0.458   8.490  12857  Z= 0.234
  Chirality :  0.037   0.148   1514
  Planarity :  0.004   0.031   1608
  Dihedral  :  4.638  60.336   1391
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 12.96 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.25), residues: 1193
  helix:  1.46 (0.19), residues: 765
  sheet: -0.77 (0.66), residues: 58
  loop :  0.12 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 213 
 HIS   0.004   0.001   HIS A 103 
 PHE   0.015   0.001   PHE A 979 
 TYR   0.025   0.001   TYR A 248 
 ARG   0.006   0.000   ARG A1274 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A  366 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8222 (mp)
REVERT: A 1046 ASP cc_start: 0.7714 (t70) cc_final: 0.7095 (t0)
REVERT: A 1248 GLN cc_start: 0.8601 (tt0) cc_final: 0.8257 (tp40)
  outliers start: 14
  outliers final: 8
  residues processed: 118
  average time/residue: 0.2263
  time to fit residues: 37.6125
Evaluate side-chains
  113 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1086 THR
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1201 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    0.1980
   chunk 13 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 97 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9990
   chunk 115 optimal weight:    0.3980
   chunk 72 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9500  Z= 0.135
  Angle     :  0.437   8.535  12857  Z= 0.223
  Chirality :  0.036   0.132   1514
  Planarity :  0.004   0.029   1608
  Dihedral  :  3.950  46.783   1391
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.06 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.25), residues: 1193
  helix:  1.49 (0.19), residues: 763
  sheet: -0.62 (0.66), residues: 58
  loop :  0.04 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 213 
 HIS   0.004   0.001   HIS A 103 
 PHE   0.009   0.001   PHE A 957 
 TYR   0.020   0.001   TYR A 248 
 ARG   0.006   0.000   ARG A1274 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A  366 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8078 (mp)
REVERT: A  634 GLN cc_start: 0.8181 (mt0) cc_final: 0.7974 (mt0)
REVERT: A 1046 ASP cc_start: 0.7669 (t70) cc_final: 0.7052 (t0)
REVERT: A 1248 GLN cc_start: 0.8600 (tt0) cc_final: 0.8255 (tp40)
  outliers start: 14
  outliers final: 8
  residues processed: 122
  average time/residue: 0.2278
  time to fit residues: 38.7927
Evaluate side-chains
  118 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue 1086 THR
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1201 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0270
   chunk 22 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0470
   chunk 57 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9500  Z= 0.131
  Angle     :  0.445   8.302  12857  Z= 0.225
  Chirality :  0.036   0.210   1514
  Planarity :  0.004   0.029   1608
  Dihedral  :  3.846  38.633   1391
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.16 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1193
  helix:  1.54 (0.19), residues: 763
  sheet: -0.50 (0.65), residues: 58
  loop :  0.10 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 213 
 HIS   0.003   0.001   HIS A 103 
 PHE   0.009   0.001   PHE A 979 
 TYR   0.020   0.001   TYR A 248 
 ARG   0.006   0.000   ARG A1274 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 1.106 
Fit side-chains
REVERT: A  366 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8040 (mp)
REVERT: A  634 GLN cc_start: 0.8158 (mt0) cc_final: 0.7956 (mt0)
REVERT: A 1017 ASP cc_start: 0.7882 (t0) cc_final: 0.7526 (t0)
REVERT: A 1046 ASP cc_start: 0.7660 (t70) cc_final: 0.7054 (t0)
REVERT: A 1248 GLN cc_start: 0.8600 (tt0) cc_final: 0.8261 (tp40)
  outliers start: 17
  outliers final: 13
  residues processed: 121
  average time/residue: 0.2335
  time to fit residues: 40.0448
Evaluate side-chains
  124 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue 1086 THR
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1201 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 110 optimal weight:    6.9990
   chunk 101 optimal weight:    0.6980
   chunk 107 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0070
   chunk 84 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0370
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
A1242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9500  Z= 0.139
  Angle     :  0.449   8.320  12857  Z= 0.228
  Chirality :  0.037   0.194   1514
  Planarity :  0.004   0.029   1608
  Dihedral  :  3.809  32.618   1391
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.35 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.25), residues: 1193
  helix:  1.56 (0.19), residues: 763
  sheet: -0.31 (0.65), residues: 58
  loop :  0.15 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 213 
 HIS   0.004   0.001   HIS A 103 
 PHE   0.009   0.001   PHE A 979 
 TYR   0.020   0.001   TYR A 248 
 ARG   0.006   0.000   ARG A1274 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 1.117 
Fit side-chains
REVERT: A  366 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8051 (mp)
REVERT: A  634 GLN cc_start: 0.8199 (mt0) cc_final: 0.7976 (mt0)
REVERT: A 1017 ASP cc_start: 0.7856 (t0) cc_final: 0.7487 (t0)
REVERT: A 1046 ASP cc_start: 0.7686 (t70) cc_final: 0.7066 (t0)
REVERT: A 1173 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6478 (pm20)
REVERT: A 1248 GLN cc_start: 0.8606 (tt0) cc_final: 0.8259 (tp40)
  outliers start: 18
  outliers final: 15
  residues processed: 120
  average time/residue: 0.2262
  time to fit residues: 37.9251
Evaluate side-chains
  128 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1086 THR
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1173 GLU
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1201 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 119 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0020
   chunk 9 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.1592

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

Flipped N/Q/H residues before XYZ refinement:
** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9500  Z= 0.227
  Angle     :  0.485   9.483  12857  Z= 0.246
  Chirality :  0.038   0.220   1514
  Planarity :  0.004   0.029   1608
  Dihedral  :  3.963  33.021   1391
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.75 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.25), residues: 1193
  helix:  1.37 (0.19), residues: 775
  sheet: -0.36 (0.65), residues: 58
  loop :  0.20 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 520 
 HIS   0.005   0.001   HIS A 103 
 PHE   0.017   0.001   PHE A 979 
 TYR   0.027   0.001   TYR A 248 
 ARG   0.003   0.000   ARG A1274 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 1.165 
Fit side-chains
REVERT: A  366 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8313 (mp)
REVERT: A  634 GLN cc_start: 0.8211 (mt0) cc_final: 0.7991 (mt0)
REVERT: A 1046 ASP cc_start: 0.7729 (t70) cc_final: 0.7077 (t0)
REVERT: A 1248 GLN cc_start: 0.8615 (tt0) cc_final: 0.8242 (tp40)
  outliers start: 15
  outliers final: 12
  residues processed: 112
  average time/residue: 0.2542
  time to fit residues: 39.8000
Evaluate side-chains
  114 residues out of total 1011 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1086 THR
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1201 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 95 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.133810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.099106 restraints weight = 11915.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.00
r_work: 0.3059 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9500  Z= 0.195
  Angle     :  0.474   9.497  12857  Z= 0.241
  Chirality :  0.038   0.192   1514
  Planarity :  0.004   0.029   1608
  Dihedral  :  3.970  32.789   1391
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.65 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.25), residues: 1193
  helix:  1.35 (0.19), residues: 775
  sheet: -0.24 (0.65), residues: 58
  loop :  0.22 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 520 
 HIS   0.005   0.001   HIS A 103 
 PHE   0.013   0.001   PHE A 979 
 TYR   0.024   0.001   TYR A 248 
 ARG   0.006   0.000   ARG A1274 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2314.09 seconds
wall clock time: 42 minutes 40.65 seconds (2560.65 seconds total)