Starting phenix.real_space_refine (version: 1.21rc1)
on Fri Oct  6 00:54:36 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/10_2023/8emv_28266.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/10_2023/8emv_28266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/10_2023/8emv_28266.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/10_2023/8emv_28266.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/10_2023/8emv_28266.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/10_2023/8emv_28266.pdb"
  }
  resolution = 3.6
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5939 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      31      5.16       5
     C    3795      2.51       5
     N    1013      2.21       5
     O    1109      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU   33": "OE1" <-> "OE2"
    Residue "A ARG   38": "NH1" <-> "NH2"
    Residue "A ARG   87": "NH1" <-> "NH2"
    Residue "A GLU   88": "OE1" <-> "OE2"
    Residue "A GLU  134": "OE1" <-> "OE2"
    Residue "A PHE  152": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  179": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  207": "OE1" <-> "OE2"
    Residue "A GLU  214": "OE1" <-> "OE2"
    Residue "A TYR  240": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  285": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  303": "OE1" <-> "OE2"
    Residue "A GLU  311": "OE1" <-> "OE2"
    Residue "A TYR  326": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  335": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  374": "OE1" <-> "OE2"
    Residue "A PHE  376": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  381": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  391": "OD1" <-> "OD2"
    Residue "A TYR  406": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  413": "OE1" <-> "OE2"
    Residue "A ASP  417": "OD1" <-> "OD2"
    Residue "A ASP  435": "OD1" <-> "OD2"
    Residue "A ASP  443": "OD1" <-> "OD2"
    Residue "A ASP  576": "OD1" <-> "OD2"
    Residue "A GLU  589": "OE1" <-> "OE2"
    Residue "A GLU  606": "OE1" <-> "OE2"
    Residue "A PHE  620": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  636": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  648": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  659": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  676": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  698": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  703": "OE1" <-> "OE2"
    Residue "A PHE  715": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  752": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  783": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  843": "OE1" <-> "OE2"
    Residue "A ARG  872": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib"
  Total number of atoms: 5949
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 748, 5949
          Unusual residues: {' CA': 1}
          Classifications: {'peptide': 747, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 47, 'TRANS': 699, None: 1}
            Not linked:
              pdbres="GLY A 881 "
              pdbres=" CA A1301 "
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
  Time building chain proxies: 3.76, per 1000 atoms: 0.63
  Number of scatterers: 5949
  At special positions: 0
  Unit cell: (62.64, 98.28, 103.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      31     16.00
     O    1109      8.00
     N    1013      7.00
     C    3795      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: 2.25
  Conformation dependent library (CDL) restraints added in 796.5 milliseconds
  

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1418

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 6 sheets defined
      33.3% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 25
      removed outlier: 3.743A  pdb=" N   ARG A  24 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 127 through 140
    Processing helix  chain 'A' and resid 148 through 163
      removed outlier: 3.503A  pdb=" N   PHE A 152 " --> pdb=" O   SER A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 179
      removed outlier: 4.287A  pdb=" N   ILE A 175 " --> pdb=" O   PRO A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 194
      removed outlier: 3.641A  pdb=" N   GLU A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 208
    Processing helix  chain 'A' and resid 209 through 221
    Processing helix  chain 'A' and resid 223 through 233
      removed outlier: 3.662A  pdb=" N   ASP A 227 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 253
    Processing helix  chain 'A' and resid 268 through 280
      removed outlier: 4.887A  pdb=" N   LEU A 274 " --> pdb=" O   SER A 270 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LEU A 275 " --> pdb=" O   GLN A 271 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ILE A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 288
      removed outlier: 3.736A  pdb=" N   GLU A 287 " --> pdb=" O   GLN A 283 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ARG A 288 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 300
      removed outlier: 3.639A  pdb=" N   ARG A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 347 through 357
      removed outlier: 3.927A  pdb=" N   ARG A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 399
    Processing helix  chain 'A' and resid 418 through 434
      removed outlier: 3.672A  pdb=" N   PHE A 433 " --> pdb=" O   CYS A 429 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY A 434 " --> pdb=" O   ARG A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 611
    Processing helix  chain 'A' and resid 622 through 632
    Processing helix  chain 'A' and resid 632 through 641
    Processing helix  chain 'A' and resid 661 through 666
    Processing helix  chain 'A' and resid 680 through 690
    Processing helix  chain 'A' and resid 702 through 706
      removed outlier: 3.674A  pdb=" N   ARG A 706 " --> pdb=" O   GLU A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 816
      No H-bonds generated for 'chain 'A' and resid 814 through 816'
    Processing helix  chain 'A' and resid 868 through 881
      removed outlier: 4.689A  pdb=" N   ALA A 878 " --> pdb=" O   ARG A 874 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   LEU A 879 " --> pdb=" O   GLN A 875 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65
      removed outlier: 4.116A  pdb=" N   THR A  55 " --> pdb=" O   THR A  42 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   THR A  42 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER A  26 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 328
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 388
      removed outlier: 6.706A  pdb=" N   VAL A 361 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   GLU A 413 " --> pdb=" O   VAL A 361 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU A 363 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 598 through 599
      removed outlier: 5.978A  pdb=" N   GLU A 598 " --> pdb=" O   MET A 617 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   SER A 619 " --> pdb=" O   GLU A 598 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU A 644 " --> pdb=" O   GLU A 616 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A 618 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 671 " --> pdb=" O   SER A 645 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 781 through 786
      removed outlier: 4.518A  pdb=" N   LYS A 785 " --> pdb=" O   ASN A 726 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASN A 726 " --> pdb=" O   LYS A 785 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LEU A 839 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   GLY A 735 " --> pdb=" O   ALA A 837 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ALA A 837 " --> pdb=" O   GLY A 735 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 759 through 763
      removed outlier: 5.058A  pdb=" N   LYS A 761 " --> pdb=" O   VAL A 749 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   VAL A 749 " --> pdb=" O   LYS A 761 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   ARG A 763 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   VAL A 747 " --> pdb=" O   ARG A 763 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   GLU A 800 " --> pdb=" O   PHE A 805 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   PHE A 805 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)

    201 hydrogen bonds defined for protein.
    570 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.56

  Time building geometry restraints manager: 2.46 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: 1898
        1.34 -     1.45: 878
        1.45 -     1.57: 3246
        1.57 -     1.69: 0
        1.69 -     1.81: 53
  Bond restraints: 6075
  Sorted by residual:
  bond pdb=" C   PRO A 370 "
       pdb=" N   PRO A 371 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.054 1.20e-02 6.94e+03 2.04e+01
  bond pdb=" C   PRO A 454 "
       pdb=" N   SER A 455 "
    ideal  model  delta    sigma   weight residual
    1.329  1.233  0.095 3.03e-02 1.09e+03 9.92e+00
  bond pdb=" C   LEU A 835 "
       pdb=" N   PRO A 836 "
    ideal  model  delta    sigma   weight residual
    1.333  1.349 -0.016 1.17e-02 7.31e+03 1.99e+00
  bond pdb=" CB  CYS A 669 "
       pdb=" SG  CYS A 669 "
    ideal  model  delta    sigma   weight residual
    1.808  1.763  0.045 3.30e-02 9.18e+02 1.85e+00
  bond pdb=" C   LEU A 453 "
       pdb=" N   PRO A 454 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.25e-02 6.40e+03 1.72e+00
  ... (remaining 6070 not shown)

  Histogram of bond angle deviations from ideal:
       99.49 -   106.39: 203
      106.39 -   113.29: 3218
      113.29 -   120.19: 2281
      120.19 -   127.09: 2463
      127.09 -   133.99: 62
  Bond angle restraints: 8227
  Sorted by residual:
  angle pdb=" C   SER A 200 "
        pdb=" N   GLU A 201 "
        pdb=" CA  GLU A 201 "
      ideal   model   delta    sigma   weight residual
     121.54  129.14   -7.60 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" C   GLY A 380 "
        pdb=" N   PHE A 381 "
        pdb=" CA  PHE A 381 "
      ideal   model   delta    sigma   weight residual
     122.82  128.33   -5.51 1.42e+00 4.96e-01 1.50e+01
  angle pdb=" N   LEU A 835 "
        pdb=" CA  LEU A 835 "
        pdb=" C   LEU A 835 "
      ideal   model   delta    sigma   weight residual
     109.81  117.69   -7.88 2.21e+00 2.05e-01 1.27e+01
  angle pdb=" N   PRO A 370 "
        pdb=" CA  PRO A 370 "
        pdb=" C   PRO A 370 "
      ideal   model   delta    sigma   weight residual
     110.70  114.57   -3.87 1.22e+00 6.72e-01 1.00e+01
  angle pdb=" CA  PRO A 370 "
        pdb=" C   PRO A 370 "
        pdb=" N   PRO A 371 "
      ideal   model   delta    sigma   weight residual
     117.93  121.50   -3.57 1.20e+00 6.94e-01 8.86e+00
  ... (remaining 8222 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.47: 3225
       16.47 -    32.94: 405
       32.94 -    49.41: 65
       49.41 -    65.88: 23
       65.88 -    82.35: 7
  Dihedral angle restraints: 3725
    sinusoidal: 1539
      harmonic: 2186
  Sorted by residual:
  dihedral pdb=" CA  LYS A 238 "
           pdb=" C   LYS A 238 "
           pdb=" N   PRO A 239 "
           pdb=" CA  PRO A 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.53  -29.47     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  LYS A 236 "
           pdb=" C   LYS A 236 "
           pdb=" N   GLY A 237 "
           pdb=" CA  GLY A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.95   24.05     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  PRO A 239 "
           pdb=" C   PRO A 239 "
           pdb=" N   TYR A 240 "
           pdb=" CA  TYR A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.69  -19.31     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 3722 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 548
       0.039 -    0.078: 254
       0.078 -    0.117: 77
       0.117 -    0.156: 26
       0.156 -    0.195: 10
  Chirality restraints: 915
  Sorted by residual:
  chirality pdb=" CB  VAL A 116 "
            pdb=" CA  VAL A 116 "
            pdb=" CG1 VAL A 116 "
            pdb=" CG2 VAL A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.19 2.00e-01 2.50e+01 9.46e-01
  chirality pdb=" CB  VAL A 621 "
            pdb=" CA  VAL A 621 "
            pdb=" CG1 VAL A 621 "
            pdb=" CG2 VAL A 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.22e-01
  chirality pdb=" CA  LEU A 835 "
            pdb=" N   LEU A 835 "
            pdb=" C   LEU A 835 "
            pdb=" CB  LEU A 835 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.71e-01
  ... (remaining 912 not shown)

  Planarity restraints: 1071
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 369 "    0.046 5.00e-02 4.00e+02   6.97e-02 7.77e+00
        pdb=" N   PRO A 370 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 370 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 370 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 111 "   -0.041 5.00e-02 4.00e+02   6.07e-02 5.89e+00
        pdb=" N   PRO A 112 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 112 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 112 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 321 "   -0.037 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO A 322 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1068 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2031
        2.85 -     3.36: 5011
        3.36 -     3.88: 9084
        3.88 -     4.39: 10476
        4.39 -     4.90: 18462
  Nonbonded interactions: 45064
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 225 "
            pdb=" OD1 ASP A 225 "
     model   vdw
     2.339 2.520
  nonbonded pdb=" O   SER A 591 "
            pdb=" OG  SER A 591 "
     model   vdw
     2.340 2.440
  nonbonded pdb=" OE1 GLU A 577 "
            pdb=" OG  SER A 581 "
     model   vdw
     2.356 2.440
  nonbonded pdb=" N   ASP A 125 "
            pdb=" OD1 ASP A 125 "
     model   vdw
     2.377 2.520
  nonbonded pdb=" O   SER A 404 "
            pdb=" OG  SER A 404 "
     model   vdw
     2.382 2.440
  ... (remaining 45059 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:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          3.990
  Check model and map are aligned:         0.090
  Set scattering table:                    0.060
  Process input model:                     19.130
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
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      :  0.007   0.095   6075  Z= 0.453
  Angle     :  0.813   8.282   8227  Z= 0.461
  Chirality :  0.052   0.195    915
  Planarity :  0.007   0.070   1071
  Dihedral  : 15.162  82.355   2307
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  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: -4.26 (0.24), residues: 739
  helix: -3.01 (0.23), residues: 235
  sheet: -2.29 (0.41), residues: 124
  loop : -2.89 (0.26), residues: 380

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.750 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2484
  time to fit residues: 24.7972
Evaluate side-chains
  55 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.715 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9758
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    0.4980
   chunk 58 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0050
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6075  Z= 0.144
  Angle     :  0.503   5.568   8227  Z= 0.265
  Chirality :  0.042   0.152    915
  Planarity :  0.005   0.044   1071
  Dihedral  :  4.629  25.862    816
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 11.93 %
    Favored  : 87.16 %
  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: -2.69 (0.27), residues: 739
  helix: -0.97 (0.31), residues: 237
  sheet: -2.02 (0.41), residues: 121
  loop : -2.24 (0.28), residues: 381

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.731 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 76
  average time/residue: 0.2094
  time to fit residues: 20.7910
Evaluate side-chains
  64 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.701 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0570
  time to fit residues: 1.3461
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 166 GLN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6075  Z= 0.228
  Angle     :  0.522   6.250   8227  Z= 0.267
  Chirality :  0.042   0.164    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  4.454  25.158    816
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.22 %
    Favored  : 84.40 %
  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: -1.96 (0.29), residues: 739
  helix: -0.10 (0.33), residues: 243
  sheet: -1.43 (0.45), residues: 121
  loop : -2.10 (0.29), residues: 375

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 71
  average time/residue: 0.2089
  time to fit residues: 19.6892
Evaluate side-chains
  67 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.718 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1156
  time to fit residues: 1.9746
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0570
   overall best weight:    1.5904

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6075  Z= 0.259
  Angle     :  0.526   5.844   8227  Z= 0.268
  Chirality :  0.043   0.158    915
  Planarity :  0.004   0.052   1071
  Dihedral  :  4.442  24.835    816
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.14 %
    Favored  : 83.18 %
  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: -1.58 (0.30), residues: 739
  helix:  0.29 (0.35), residues: 244
  sheet: -1.12 (0.44), residues: 125
  loop : -1.98 (0.30), residues: 370

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.735 
Fit side-chains
  outliers start: 11
  outliers final: 6
  residues processed: 67
  average time/residue: 0.1803
  time to fit residues: 16.6242
Evaluate side-chains
  62 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.737 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0602
  time to fit residues: 1.6568
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6075  Z= 0.186
  Angle     :  0.498   6.209   8227  Z= 0.253
  Chirality :  0.042   0.162    915
  Planarity :  0.004   0.052   1071
  Dihedral  :  4.234  23.832    816
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 15.44 %
    Favored  : 83.03 %
  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: -1.16 (0.31), residues: 739
  helix:  0.67 (0.35), residues: 239
  sheet: -0.91 (0.44), residues: 124
  loop : -1.71 (0.31), residues: 376

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 3
  residues processed: 68
  average time/residue: 0.1869
  time to fit residues: 17.4618
Evaluate side-chains
  58 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.786 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0722
  time to fit residues: 1.4323
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    0.0870
   chunk 64 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6075  Z= 0.256
  Angle     :  0.525   6.440   8227  Z= 0.267
  Chirality :  0.043   0.157    915
  Planarity :  0.004   0.052   1071
  Dihedral  :  4.315  24.224    816
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 17.28 %
    Favored  : 81.80 %
  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: -1.13 (0.31), residues: 739
  helix:  0.82 (0.36), residues: 238
  sheet: -0.91 (0.43), residues: 125
  loop : -1.77 (0.30), residues: 376

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.734 
Fit side-chains
  outliers start: 6
  outliers final: 1
  residues processed: 59
  average time/residue: 0.2030
  time to fit residues: 16.1924
Evaluate side-chains
  56 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.742 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0604
  time to fit residues: 1.0640
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 71 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6075  Z= 0.321
  Angle     :  0.558   6.768   8227  Z= 0.283
  Chirality :  0.044   0.157    915
  Planarity :  0.004   0.053   1071
  Dihedral  :  4.476  23.987    816
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.06 %
    Favored  : 81.50 %
  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: -1.13 (0.31), residues: 739
  helix:  0.79 (0.36), residues: 238
  sheet: -0.91 (0.43), residues: 125
  loop : -1.75 (0.31), residues: 376

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.734 
Fit side-chains
  outliers start: 16
  outliers final: 10
  residues processed: 68
  average time/residue: 0.1749
  time to fit residues: 16.6681
Evaluate side-chains
  65 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.745 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0641
  time to fit residues: 2.1546
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
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      :  0.003   0.028   6075  Z= 0.165
  Angle     :  0.502   7.364   8227  Z= 0.253
  Chirality :  0.042   0.157    915
  Planarity :  0.004   0.052   1071
  Dihedral  :  4.163  22.305    816
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 16.51 %
    Favored  : 82.72 %
  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: -0.77 (0.31), residues: 739
  helix:  1.14 (0.36), residues: 232
  sheet: -0.78 (0.44), residues: 125
  loop : -1.50 (0.31), residues: 382

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.845 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 61
  average time/residue: 0.2275
  time to fit residues: 18.2261
Evaluate side-chains
  57 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.725 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0611
  time to fit residues: 1.2155
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   chunk 43 optimal weight:    0.2980
   chunk 70 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0770
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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: 0.8123
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6075  Z= 0.126
  Angle     :  0.482   7.819   8227  Z= 0.242
  Chirality :  0.041   0.153    915
  Planarity :  0.004   0.051   1071
  Dihedral  :  3.865  21.182    816
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 17.28 %
    Favored  : 82.26 %
  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: -0.58 (0.32), residues: 739
  helix:  1.31 (0.37), residues: 233
  sheet: -0.85 (0.44), residues: 125
  loop : -1.31 (0.32), residues: 381

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 64
  average time/residue: 0.2275
  time to fit residues: 18.9940
Evaluate side-chains
  60 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 0.727 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0678
  time to fit residues: 1.2365
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0170
   chunk 46 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6075  Z= 0.133
  Angle     :  0.485   7.917   8227  Z= 0.244
  Chirality :  0.041   0.157    915
  Planarity :  0.004   0.051   1071
  Dihedral  :  3.834  21.206    816
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 17.74 %
    Favored  : 81.96 %
  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: -0.43 (0.32), residues: 739
  helix:  1.39 (0.36), residues: 233
  sheet: -0.71 (0.44), residues: 121
  loop : -1.22 (0.32), residues: 385

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 64
  average time/residue: 0.2262
  time to fit residues: 19.1132
Evaluate side-chains
  60 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.746 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0905
  time to fit residues: 1.1622
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    0.0020
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** 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 = 0.3226 r_free = 0.3226 target = 0.109418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.085091 restraints weight = 9025.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.087336 restraints weight = 6112.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.088654 restraints weight = 4775.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6075  Z= 0.140
  Angle     :  0.490   7.895   8227  Z= 0.247
  Chirality :  0.041   0.150    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  3.810  20.920    816
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 18.35 %
    Favored  : 81.50 %
  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: -0.35 (0.32), residues: 739
  helix:  1.46 (0.36), residues: 233
  sheet: -0.70 (0.44), residues: 121
  loop : -1.15 (0.32), residues: 385
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1376.85 seconds
wall clock time: 25 minutes 44.13 seconds (1544.13 seconds total)