Starting phenix.real_space_refine
on Mon Mar 11 07:56:17 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/03_2024/7ptx_13642.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/03_2024/7ptx_13642.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/03_2024/7ptx_13642.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/03_2024/7ptx_13642.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/03_2024/7ptx_13642.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/03_2024/7ptx_13642.pdb"
  }
  resolution = 4.03
  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=   0.001
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      23      5.16       5
     C    4829      2.51       5
     N    1334      2.21       5
     O    1467      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP  574": "OD1" <-> "OD2"
    Residue "A TYR  683": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  872": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  879": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  988": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 7653
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1000, 7653
          Classifications: {'peptide': 1000}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 31, 'TRANS': 968}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 243
          Unresolved non-hydrogen angles: 306
          Unresolved non-hydrogen dihedrals: 208
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 156
  Time building chain proxies: 4.57, per 1000 atoms: 0.60
  Number of scatterers: 7653
  At special positions: 0
  Unit cell: (123.3, 127.8, 90, 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      23     16.00
     O    1467      8.00
     N    1334      7.00
     C    4829      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: 3.18
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1898

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 2 sheets defined
      64.2% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 57
      removed outlier: 3.585A  pdb=" N   VAL A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 62
      removed outlier: 4.185A  pdb=" N   GLY A  61 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ALA A  62 " --> pdb=" O   ILE A  59 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 58 through 62'
    Processing helix  chain 'A' and resid 66 through 77
      removed outlier: 3.708A  pdb=" N   ALA A  70 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 86
    Processing helix  chain 'A' and resid 90 through 109
    Processing helix  chain 'A' and resid 119 through 147
      removed outlier: 4.018A  pdb=" N   GLU A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU A 142 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLY A 143 " --> pdb=" O   GLU A 139 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   HIS A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A 147 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 151
      removed outlier: 3.506A  pdb=" N   ILE A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 148 through 151'
    Processing helix  chain 'A' and resid 157 through 178
      removed outlier: 3.739A  pdb=" N   GLU A 175 " --> pdb=" O   ASN A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 190
    Processing helix  chain 'A' and resid 196 through 204
      removed outlier: 4.502A  pdb=" N   SER A 204 " --> pdb=" O   TYR A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 225
      removed outlier: 3.821A  pdb=" N   LEU A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   SER A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   LEU A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ALA A 225 " --> pdb=" O   ASN A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 269
    Processing helix  chain 'A' and resid 272 through 296
    Processing helix  chain 'A' and resid 304 through 320
      removed outlier: 3.750A  pdb=" N   ARG A 320 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 348
      removed outlier: 3.763A  pdb=" N   ASN A 328 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LYS A 335 " --> pdb=" O   GLN A 331 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   SER A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   THR A 348 " --> pdb=" O   ARG A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 468
    Processing helix  chain 'A' and resid 470 through 484
      removed outlier: 4.159A  pdb=" N   GLY A 476 " --> pdb=" O   GLU A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 506
    Processing helix  chain 'A' and resid 508 through 515
    Processing helix  chain 'A' and resid 517 through 524
      removed outlier: 3.544A  pdb=" N   LEU A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN A 523 " --> pdb=" O   ASN A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 541 through 550
      removed outlier: 3.878A  pdb=" N   GLU A 550 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 571
      removed outlier: 3.686A  pdb=" N   ALA A 571 " --> pdb=" O   LEU A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 584
    Processing helix  chain 'A' and resid 601 through 608
      removed outlier: 3.975A  pdb=" N   ILE A 605 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   THR A 606 " --> pdb=" O   LEU A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 618
      removed outlier: 4.369A  pdb=" N   ARG A 613 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ASN A 617 " --> pdb=" O   ARG A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 640
    Processing helix  chain 'A' and resid 642 through 653
      removed outlier: 4.250A  pdb=" N   ASN A 653 " --> pdb=" O   LEU A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 676
    Processing helix  chain 'A' and resid 677 through 687
    Processing helix  chain 'A' and resid 702 through 710
    Processing helix  chain 'A' and resid 713 through 723
      removed outlier: 4.051A  pdb=" N   ARG A 723 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 735
      removed outlier: 4.400A  pdb=" N   ALA A 734 " --> pdb=" O   ARG A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 745
      removed outlier: 3.884A  pdb=" N   LEU A 740 " --> pdb=" O   THR A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 756
    Processing helix  chain 'A' and resid 769 through 777
      removed outlier: 3.883A  pdb=" N   LEU A 773 " --> pdb=" O   THR A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 789
      removed outlier: 4.254A  pdb=" N   GLN A 784 " --> pdb=" O   THR A 780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 811
      removed outlier: 4.173A  pdb=" N   PHE A 806 " --> pdb=" O   THR A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 822
    Processing helix  chain 'A' and resid 835 through 844
      removed outlier: 3.840A  pdb=" N   GLU A 839 " --> pdb=" O   MET A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 857
      removed outlier: 4.094A  pdb=" N   VAL A 849 " --> pdb=" O   HIS A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 861
    Processing helix  chain 'A' and resid 870 through 878
    Processing helix  chain 'A' and resid 879 through 889
    Processing helix  chain 'A' and resid 893 through 897
      removed outlier: 3.582A  pdb=" N   ASN A 897 " --> pdb=" O   ASN A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 902 through 908
      removed outlier: 3.753A  pdb=" N   SER A 908 " --> pdb=" O   LEU A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 911
      No H-bonds generated for 'chain 'A' and resid 909 through 911'
    Processing helix  chain 'A' and resid 914 through 921
    Processing helix  chain 'A' and resid 935 through 943
      removed outlier: 3.695A  pdb=" N   PHE A 943 " --> pdb=" O   LEU A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 955
      removed outlier: 4.015A  pdb=" N   VAL A 949 " --> pdb=" O   HIS A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 980
      removed outlier: 3.741A  pdb=" N   CYS A 975 " --> pdb=" O   TYR A 971 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ASP A 976 " --> pdb=" O   HIS A 972 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER A 977 " --> pdb=" O   ALA A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 992
    Processing helix  chain 'A' and resid 999 through 1007
      removed outlier: 3.738A  pdb=" N   GLU A1003 " --> pdb=" O   SER A 999 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR A1007 " --> pdb=" O   GLU A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1021
    Processing helix  chain 'A' and resid 1034 through 1042
    Processing helix  chain 'A' and resid 1054 through 1065
      removed outlier: 3.920A  pdb=" N   VAL A1059 " --> pdb=" O   GLU A1055 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   VAL A1060 " --> pdb=" O   ARG A1056 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU A1061 " --> pdb=" O   LEU A1057 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TYR A1062 " --> pdb=" O   ASP A1058 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 373
    Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 403

    388 hydrogen bonds defined for protein.
    1140 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: 2.24

  Time building geometry restraints manager: 3.41 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: 2577
        1.34 -     1.46: 1185
        1.46 -     1.58: 3976
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 7777
  Sorted by residual:
  bond pdb=" C   ASN A 419 "
       pdb=" N   PRO A 420 "
    ideal  model  delta    sigma   weight residual
    1.332  1.355 -0.023 1.12e-02 7.97e+03 4.32e+00
  bond pdb=" CB  PRO A 737 "
       pdb=" CG  PRO A 737 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.30e+00
  bond pdb=" C   THR A 782 "
       pdb=" N   PRO A 783 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 2.34e-02 1.83e+03 1.46e+00
  bond pdb=" CG  MET A 283 "
       pdb=" SD  MET A 283 "
    ideal  model  delta    sigma   weight residual
    1.803  1.778  0.025 2.50e-02 1.60e+03 9.65e-01
  bond pdb=" CG  GLU A 876 "
       pdb=" CD  GLU A 876 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 9.64e-01
  ... (remaining 7772 not shown)

  Histogram of bond angle deviations from ideal:
       99.30 -   106.24: 151
      106.24 -   113.17: 4253
      113.17 -   120.10: 2783
      120.10 -   127.04: 3297
      127.04 -   133.97: 53
  Bond angle restraints: 10537
  Sorted by residual:
  angle pdb=" CA  PRO A 737 "
        pdb=" N   PRO A 737 "
        pdb=" CD  PRO A 737 "
      ideal   model   delta    sigma   weight residual
     112.00  106.07    5.93 1.40e+00 5.10e-01 1.79e+01
  angle pdb=" N   VAL A  65 "
        pdb=" CA  VAL A  65 "
        pdb=" C   VAL A  65 "
      ideal   model   delta    sigma   weight residual
     112.80  108.59    4.21 1.15e+00 7.56e-01 1.34e+01
  angle pdb=" C   ILE A 832 "
        pdb=" N   ASN A 833 "
        pdb=" CA  ASN A 833 "
      ideal   model   delta    sigma   weight residual
     122.46  127.43   -4.97 1.41e+00 5.03e-01 1.24e+01
  angle pdb=" C   HIS A 282 "
        pdb=" N   MET A 283 "
        pdb=" CA  MET A 283 "
      ideal   model   delta    sigma   weight residual
     121.14  115.15    5.99 1.75e+00 3.27e-01 1.17e+01
  angle pdb=" N   GLU A 876 "
        pdb=" CA  GLU A 876 "
        pdb=" CB  GLU A 876 "
      ideal   model   delta    sigma   weight residual
     110.39  116.05   -5.66 1.66e+00 3.63e-01 1.16e+01
  ... (remaining 10532 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.46: 4195
       16.46 -    32.91: 441
       32.91 -    49.37: 80
       49.37 -    65.83: 13
       65.83 -    82.28: 7
  Dihedral angle restraints: 4736
    sinusoidal: 1814
      harmonic: 2922
  Sorted by residual:
  dihedral pdb=" CA  LYS A 934 "
           pdb=" C   LYS A 934 "
           pdb=" N   SER A 935 "
           pdb=" CA  SER A 935 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.28  -22.72     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  LYS A 699 "
           pdb=" C   LYS A 699 "
           pdb=" N   ASN A 700 "
           pdb=" CA  ASN A 700 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.60   22.40     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  THR A 992 "
           pdb=" C   THR A 992 "
           pdb=" N   LEU A 993 "
           pdb=" CA  LEU A 993 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.02  -21.98     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 4733 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 719
       0.034 -    0.068: 353
       0.068 -    0.102: 105
       0.102 -    0.135: 36
       0.135 -    0.169: 11
  Chirality restraints: 1224
  Sorted by residual:
  chirality pdb=" CA  GLU A 134 "
            pdb=" N   GLU A 134 "
            pdb=" C   GLU A 134 "
            pdb=" CB  GLU A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CA  PRO A 737 "
            pdb=" N   PRO A 737 "
            pdb=" C   PRO A 737 "
            pdb=" CB  PRO A 737 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.44e-01
  chirality pdb=" CB  VAL A  56 "
            pdb=" CA  VAL A  56 "
            pdb=" CG1 VAL A  56 "
            pdb=" CG2 VAL A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.42e-01
  ... (remaining 1221 not shown)

  Planarity restraints: 1381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 736 "   -0.064 5.00e-02 4.00e+02   9.42e-02 1.42e+01
        pdb=" N   PRO A 737 "    0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO A 737 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 737 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 441 "   -0.041 5.00e-02 4.00e+02   6.23e-02 6.20e+00
        pdb=" N   PRO A 442 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 442 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 442 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 632 "   -0.033 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO A 633 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 633 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 633 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1378 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 883
        2.74 -     3.28: 9100
        3.28 -     3.82: 13154
        3.82 -     4.36: 15240
        4.36 -     4.90: 23646
  Nonbonded interactions: 62023
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 367 "
            pdb=" NZ  LYS A 407 "
     model   vdw
     2.203 2.520
  nonbonded pdb=" NH2 ARG A 512 "
            pdb=" O   PHE A 544 "
     model   vdw
     2.209 2.520
  nonbonded pdb=" O   GLU A 493 "
            pdb=" NZ  LYS A 527 "
     model   vdw
     2.243 2.520
  nonbonded pdb=" O   ARG A 610 "
            pdb=" OG1 THR A 614 "
     model   vdw
     2.250 2.440
  nonbonded pdb=" O   ASN A 439 "
            pdb=" NZ  LYS A 441 "
     model   vdw
     2.252 2.520
  ... (remaining 62018 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.580
  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:          9.710
  Check model and map are aligned:         0.100
  Set scattering table:                    0.070
  Process input model:                     25.040
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   7777  Z= 0.215
  Angle     :  0.756   8.972  10537  Z= 0.411
  Chirality :  0.045   0.169   1224
  Planarity :  0.005   0.094   1381
  Dihedral  : 14.083  82.282   2838
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 19.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  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: -1.97 (0.26), residues: 994
  helix: -0.39 (0.21), residues: 575
  sheet: -3.62 (0.77), residues: 35
  loop : -2.46 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 384 
 HIS   0.004   0.001   HIS A 972 
 PHE   0.020   0.001   PHE A 290 
 TYR   0.025   0.002   TYR A 951 
 ARG   0.005   0.000   ARG A 512 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  666 MET cc_start: 0.7947 (ppp) cc_final: 0.6675 (ppp)
REVERT: A  901 ASN cc_start: 0.8547 (p0) cc_final: 0.8330 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1793
  time to fit residues: 29.4778
Evaluate side-chains
  90 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.0470
   chunk 75 optimal weight:    0.2980
   chunk 42 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 90 optimal weight:    8.9990
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 897 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7777  Z= 0.171
  Angle     :  0.629   6.691  10537  Z= 0.329
  Chirality :  0.042   0.152   1224
  Planarity :  0.005   0.058   1381
  Dihedral  :  5.342  20.919   1058
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  7.44 %
    Favored  : 92.06 %
  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 (0.26), residues: 994
  helix:  0.03 (0.21), residues: 581
  sheet: -3.30 (0.78), residues: 35
  loop : -2.33 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 384 
 HIS   0.005   0.001   HIS A 459 
 PHE   0.017   0.001   PHE A 290 
 TYR   0.024   0.002   TYR A 872 
 ARG   0.006   0.000   ARG A 512 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 119
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A   84 MET cc_start: 0.7463 (tpt) cc_final: 0.6892 (tpp)
REVERT: A   95 ASP cc_start: 0.8218 (t0) cc_final: 0.8002 (t0)
REVERT: A  461 ASP cc_start: 0.7641 (m-30) cc_final: 0.7322 (m-30)
REVERT: A  666 MET cc_start: 0.8227 (ppp) cc_final: 0.7646 (ppp)
REVERT: A 1011 ASP cc_start: 0.8788 (p0) cc_final: 0.8201 (p0)
REVERT: A 1012 LEU cc_start: 0.9247 (mm) cc_final: 0.8978 (mm)
  outliers start: 4
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1874
  time to fit residues: 31.7086
Evaluate side-chains
  89 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 90 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0970
   chunk 72 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 721 GLN
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7777  Z= 0.185
  Angle     :  0.629   5.925  10537  Z= 0.332
  Chirality :  0.042   0.152   1224
  Planarity :  0.004   0.055   1381
  Dihedral  :  5.293  21.253   1058
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  7.44 %
    Favored  : 92.18 %
  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: -1.36 (0.26), residues: 994
  helix:  0.13 (0.21), residues: 580
  sheet: -2.95 (0.84), residues: 35
  loop : -2.31 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 384 
 HIS   0.005   0.001   HIS A1009 
 PHE   0.019   0.002   PHE A 290 
 TYR   0.020   0.002   TYR A 872 
 ARG   0.009   0.000   ARG A 512 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.7522 (tpt) cc_final: 0.6924 (tpp)
REVERT: A   87 MET cc_start: 0.7697 (ttt) cc_final: 0.7360 (tmm)
REVERT: A   95 ASP cc_start: 0.8248 (t0) cc_final: 0.8046 (t0)
REVERT: A  283 MET cc_start: 0.9121 (pmm) cc_final: 0.8664 (pmm)
REVERT: A  461 ASP cc_start: 0.7557 (m-30) cc_final: 0.7250 (m-30)
REVERT: A  494 MET cc_start: 0.6507 (mpp) cc_final: 0.6281 (mpp)
REVERT: A  717 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7139 (pm20)
REVERT: A  776 MET cc_start: 0.8799 (mpp) cc_final: 0.8517 (mpp)
REVERT: A  851 MET cc_start: 0.8787 (mtm) cc_final: 0.8549 (mtt)
REVERT: A 1011 ASP cc_start: 0.8804 (p0) cc_final: 0.8431 (p0)
REVERT: A 1012 LEU cc_start: 0.9233 (mm) cc_final: 0.8959 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1768
  time to fit residues: 30.2326
Evaluate side-chains
  90 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 96 optimal weight:    0.5980
   chunk 86 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7777  Z= 0.187
  Angle     :  0.640   7.274  10537  Z= 0.336
  Chirality :  0.043   0.144   1224
  Planarity :  0.005   0.055   1381
  Dihedral  :  5.309  21.054   1058
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 18.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.06 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  4.71 %
    Favored  : 95.04 %
  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: -1.27 (0.26), residues: 994
  helix:  0.22 (0.22), residues: 576
  sheet: -2.76 (0.88), residues: 35
  loop : -2.30 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 384 
 HIS   0.004   0.001   HIS A 772 
 PHE   0.020   0.002   PHE A 290 
 TYR   0.011   0.001   TYR A 872 
 ARG   0.009   0.001   ARG A 496 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 MET cc_start: 0.9221 (pmm) cc_final: 0.8406 (pmm)
REVERT: A  334 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8603 (tp)
REVERT: A  461 ASP cc_start: 0.7665 (m-30) cc_final: 0.7342 (m-30)
REVERT: A  776 MET cc_start: 0.8874 (mpp) cc_final: 0.8586 (mpp)
REVERT: A  851 MET cc_start: 0.8771 (mtm) cc_final: 0.8517 (mtt)
REVERT: A  865 MET cc_start: 0.7583 (tpp) cc_final: 0.7194 (tpp)
REVERT: A 1011 ASP cc_start: 0.8875 (p0) cc_final: 0.8362 (p0)
REVERT: A 1012 LEU cc_start: 0.9326 (mm) cc_final: 0.9044 (mm)
REVERT: A 1015 TYR cc_start: 0.8797 (m-80) cc_final: 0.8596 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2068
  time to fit residues: 35.5196
Evaluate side-chains
  90 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.0970
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 0 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 HIS
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7777  Z= 0.187
  Angle     :  0.654   7.746  10537  Z= 0.341
  Chirality :  0.043   0.149   1224
  Planarity :  0.004   0.053   1381
  Dihedral  :  5.260  20.918   1058
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.85 %
    Favored  : 96.03 %
  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: -1.26 (0.26), residues: 994
  helix:  0.20 (0.22), residues: 576
  sheet: -2.50 (0.92), residues: 35
  loop : -2.27 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 384 
 HIS   0.009   0.001   HIS A 705 
 PHE   0.021   0.001   PHE A 290 
 TYR   0.021   0.002   TYR A 130 
 ARG   0.007   0.000   ARG A 496 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.6998 (ttt) cc_final: 0.6602 (tmm)
REVERT: A  334 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8532 (tp)
REVERT: A  461 ASP cc_start: 0.7669 (m-30) cc_final: 0.7361 (m-30)
REVERT: A  675 LEU cc_start: 0.7948 (mm) cc_final: 0.7566 (mm)
REVERT: A  776 MET cc_start: 0.8767 (mpp) cc_final: 0.8495 (mpp)
REVERT: A  851 MET cc_start: 0.8739 (mtm) cc_final: 0.8454 (mtt)
REVERT: A  865 MET cc_start: 0.7622 (tpp) cc_final: 0.7073 (tpp)
REVERT: A 1009 HIS cc_start: 0.7804 (m90) cc_final: 0.7556 (m90)
REVERT: A 1011 ASP cc_start: 0.8881 (p0) cc_final: 0.8149 (p0)
REVERT: A 1012 LEU cc_start: 0.9315 (mm) cc_final: 0.8900 (mm)
REVERT: A 1015 TYR cc_start: 0.8820 (m-80) cc_final: 0.8504 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1883
  time to fit residues: 31.7939
Evaluate side-chains
  91 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 56 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0000
   chunk 96 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 93 optimal weight:    0.4980
   chunk 10 optimal weight:    0.1980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 897 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7777  Z= 0.186
  Angle     :  0.652   8.144  10537  Z= 0.338
  Chirality :  0.043   0.152   1224
  Planarity :  0.004   0.052   1381
  Dihedral  :  5.190  21.174   1058
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.98 %
    Favored  : 96.90 %
  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: -1.17 (0.26), residues: 994
  helix:  0.21 (0.22), residues: 577
  sheet: -2.26 (0.95), residues: 35
  loop : -2.15 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 384 
 HIS   0.003   0.001   HIS A 267 
 PHE   0.019   0.001   PHE A 290 
 TYR   0.023   0.001   TYR A 971 
 ARG   0.005   0.000   ARG A 496 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.6903 (ttt) cc_final: 0.6483 (tmm)
REVERT: A  461 ASP cc_start: 0.7656 (m-30) cc_final: 0.7353 (m-30)
REVERT: A  675 LEU cc_start: 0.7965 (mm) cc_final: 0.7529 (mm)
REVERT: A  776 MET cc_start: 0.8773 (mpp) cc_final: 0.8487 (mpp)
REVERT: A  851 MET cc_start: 0.8797 (mtm) cc_final: 0.8349 (mtt)
REVERT: A  852 LEU cc_start: 0.8509 (pp) cc_final: 0.8112 (tt)
REVERT: A  865 MET cc_start: 0.7570 (tpp) cc_final: 0.6939 (tpp)
REVERT: A 1011 ASP cc_start: 0.8646 (p0) cc_final: 0.8162 (p0)
REVERT: A 1012 LEU cc_start: 0.9228 (mm) cc_final: 0.8923 (mm)
REVERT: A 1015 TYR cc_start: 0.8806 (m-10) cc_final: 0.8588 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 129
  average time/residue: 0.1944
  time to fit residues: 34.2896
Evaluate side-chains
  91 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    0.1980
   chunk 70 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   7777  Z= 0.213
  Angle     :  0.674   8.414  10537  Z= 0.351
  Chirality :  0.044   0.184   1224
  Planarity :  0.004   0.052   1381
  Dihedral  :  5.291  20.754   1058
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 18.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.21 (0.26), residues: 994
  helix:  0.17 (0.21), residues: 578
  sheet: -1.98 (1.00), residues: 33
  loop : -2.20 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 701 
 HIS   0.004   0.001   HIS A 267 
 PHE   0.023   0.002   PHE A 290 
 TYR   0.019   0.001   TYR A 130 
 ARG   0.004   0.000   ARG A 512 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.6940 (ttt) cc_final: 0.6505 (tmm)
REVERT: A  283 MET cc_start: 0.9080 (pmm) cc_final: 0.8807 (pmm)
REVERT: A  461 ASP cc_start: 0.7648 (m-30) cc_final: 0.7346 (m-30)
REVERT: A  776 MET cc_start: 0.8836 (mpp) cc_final: 0.8556 (mpp)
REVERT: A  848 ILE cc_start: 0.8538 (mp) cc_final: 0.8181 (tp)
REVERT: A  852 LEU cc_start: 0.8452 (pp) cc_final: 0.8045 (tt)
REVERT: A  865 MET cc_start: 0.7543 (tpp) cc_final: 0.6848 (tpp)
REVERT: A 1011 ASP cc_start: 0.8711 (p0) cc_final: 0.8221 (p0)
REVERT: A 1012 LEU cc_start: 0.9233 (mm) cc_final: 0.8926 (mm)
REVERT: A 1015 TYR cc_start: 0.8845 (m-10) cc_final: 0.8644 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1939
  time to fit residues: 32.4651
Evaluate side-chains
  89 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 8 optimal weight:    0.3980
   chunk 75 optimal weight:    0.9980
   chunk 87 optimal weight:    0.1980
   chunk 92 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0370
   chunk 89 optimal weight:    0.0470
   overall best weight:    0.2556

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   7777  Z= 0.189
  Angle     :  0.683   8.935  10537  Z= 0.350
  Chirality :  0.044   0.188   1224
  Planarity :  0.004   0.052   1381
  Dihedral  :  5.162  21.198   1058
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 16.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  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: -1.15 (0.26), residues: 994
  helix:  0.23 (0.21), residues: 580
  sheet: -1.76 (0.99), residues: 35
  loop : -2.22 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 701 
 HIS   0.004   0.001   HIS A 772 
 PHE   0.024   0.001   PHE A 290 
 TYR   0.035   0.002   TYR A 971 
 ARG   0.004   0.000   ARG A 344 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.6758 (ttt) cc_final: 0.6414 (tmm)
REVERT: A  283 MET cc_start: 0.8998 (pmm) cc_final: 0.8717 (pmm)
REVERT: A  461 ASP cc_start: 0.7707 (m-30) cc_final: 0.7445 (m-30)
REVERT: A  675 LEU cc_start: 0.7998 (mm) cc_final: 0.7463 (mm)
REVERT: A  740 LEU cc_start: 0.8990 (mt) cc_final: 0.8691 (mm)
REVERT: A  848 ILE cc_start: 0.8515 (mp) cc_final: 0.8182 (mp)
REVERT: A  852 LEU cc_start: 0.8315 (pp) cc_final: 0.8047 (tt)
REVERT: A  865 MET cc_start: 0.7566 (tpp) cc_final: 0.6940 (tpp)
REVERT: A 1011 ASP cc_start: 0.8712 (p0) cc_final: 0.8145 (p0)
REVERT: A 1012 LEU cc_start: 0.9290 (mm) cc_final: 0.8977 (mm)
REVERT: A 1015 TYR cc_start: 0.8820 (m-10) cc_final: 0.8609 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2015
  time to fit residues: 33.5882
Evaluate side-chains
  93 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   7777  Z= 0.219
  Angle     :  0.704   8.888  10537  Z= 0.364
  Chirality :  0.045   0.177   1224
  Planarity :  0.004   0.053   1381
  Dihedral  :  5.294  20.946   1058
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 19.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  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: -1.18 (0.26), residues: 994
  helix:  0.17 (0.21), residues: 581
  sheet: -1.71 (1.03), residues: 33
  loop : -2.18 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 701 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.024   0.002   PHE A 907 
 TYR   0.023   0.002   TYR A 879 
 ARG   0.005   0.000   ARG A 512 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.6856 (ttt) cc_final: 0.6465 (tmm)
REVERT: A  283 MET cc_start: 0.9148 (pmm) cc_final: 0.8888 (pmm)
REVERT: A  461 ASP cc_start: 0.7641 (m-30) cc_final: 0.7356 (m-30)
REVERT: A  666 MET cc_start: 0.8134 (ppp) cc_final: 0.7907 (ppp)
REVERT: A  852 LEU cc_start: 0.8359 (pp) cc_final: 0.8134 (tt)
REVERT: A  865 MET cc_start: 0.7644 (tpp) cc_final: 0.7017 (tpp)
REVERT: A 1009 HIS cc_start: 0.7710 (m90) cc_final: 0.7492 (m90)
REVERT: A 1011 ASP cc_start: 0.8816 (p0) cc_final: 0.8190 (p0)
REVERT: A 1012 LEU cc_start: 0.9259 (mm) cc_final: 0.8924 (mm)
REVERT: A 1015 TYR cc_start: 0.8879 (m-10) cc_final: 0.8649 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1855
  time to fit residues: 30.9067
Evaluate side-chains
  93 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0370
   chunk 91 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0770
   chunk 8 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   7777  Z= 0.209
  Angle     :  0.716   8.922  10537  Z= 0.366
  Chirality :  0.045   0.176   1224
  Planarity :  0.004   0.052   1381
  Dihedral  :  5.291  21.374   1058
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 17.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  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: -1.17 (0.27), residues: 994
  helix:  0.13 (0.21), residues: 590
  sheet: -0.66 (1.31), residues: 23
  loop : -2.22 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 701 
 HIS   0.007   0.001   HIS A 213 
 PHE   0.033   0.002   PHE A 290 
 TYR   0.028   0.002   TYR A 971 
 ARG   0.003   0.000   ARG A 326 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.6821 (ttt) cc_final: 0.6428 (tmm)
REVERT: A  461 ASP cc_start: 0.7606 (m-30) cc_final: 0.7323 (m-30)
REVERT: A  773 LEU cc_start: 0.9009 (tp) cc_final: 0.8327 (tp)
REVERT: A  776 MET cc_start: 0.8713 (mpp) cc_final: 0.8451 (mpp)
REVERT: A  851 MET cc_start: 0.8737 (mtm) cc_final: 0.8471 (mtt)
REVERT: A  865 MET cc_start: 0.7638 (tpp) cc_final: 0.7016 (tpp)
REVERT: A  934 LYS cc_start: 0.8179 (tttm) cc_final: 0.6992 (tttm)
REVERT: A 1011 ASP cc_start: 0.8846 (p0) cc_final: 0.8211 (p0)
REVERT: A 1012 LEU cc_start: 0.9276 (mm) cc_final: 0.8924 (mm)
REVERT: A 1015 TYR cc_start: 0.8860 (m-10) cc_final: 0.8631 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1897
  time to fit residues: 31.2138
Evaluate side-chains
  93 residues out of total 862 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.079952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.068283 restraints weight = 44204.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.069899 restraints weight = 29076.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.071069 restraints weight = 21090.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   7777  Z= 0.218
  Angle     :  0.723  10.130  10537  Z= 0.369
  Chirality :  0.045   0.173   1224
  Planarity :  0.004   0.051   1381
  Dihedral  :  5.361  21.475   1058
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 19.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  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: -1.27 (0.26), residues: 994
  helix:  0.05 (0.21), residues: 590
  sheet: -0.74 (1.29), residues: 23
  loop : -2.28 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 701 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.024   0.002   PHE A 907 
 TYR   0.016   0.002   TYR A 951 
 ARG   0.005   0.000   ARG A 512 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1904.50 seconds
wall clock time: 35 minutes 25.34 seconds (2125.34 seconds total)