Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 17:39:16 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/04_2023/7n72_24217_trim.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/04_2023/7n72_24217.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/04_2023/7n72_24217.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/04_2023/7n72_24217.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/04_2023/7n72_24217_trim.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/04_2023/7n72_24217_trim.pdb"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
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: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       1      5.49       5
     Mg      1      5.21       5
     S      46      5.16       5
     C    5001      2.51       5
     N    1287      2.21       5
     O    1364      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 7705
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1046, 7705
          Unusual residues: {' MG': 1, 'ALF': 1, 'LMT': 3, 'PC1': 2, 'SPM': 1, 'Y01': 3}
          Classifications: {'peptide': 1030, 'undetermined': 11, 'water': 5}
          Incomplete info: {'truncation_to_alanine': 135}
          Link IDs: {'PCIS': 3, 'PTRANS': 68, 'TRANS': 958, None: 16}
            Not linked:
              pdbres="PRO A1168 "
              pdbres="ALF A1201 "
            Not linked:
              pdbres="ALF A1201 "
              pdbres=" MG A1202 "
            Not linked:
              pdbres=" MG A1202 "
              pdbres="SPM A1203 "
            Not linked:
              pdbres="SPM A1203 "
              pdbres="Y01 A1204 "
            Not linked:
              pdbres="Y01 A1204 "
              pdbres="Y01 A1205 "
            ... (remaining 11 not shown)
          Chain breaks: 6
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 623
          Unresolved non-hydrogen angles: 811
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 71
          Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 6, 'HIS:plan': 2, 'PC1:plan-2': 1, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 17}
          Unresolved non-hydrogen planarities: 294
  Time building chain proxies: 4.69, per 1000 atoms: 0.61
  Number of scatterers: 7705
  At special positions: 0
  Unit cell: (80.773, 104.9, 135.321, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      46     16.00
     P       1     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1364      8.00
     N    1287      7.00
     C    5001      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.23
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1922

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 8 sheets defined
      52.8% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 56
    Processing helix  chain 'A' and resid 59 through 68
      removed outlier: 3.799A  pdb=" N   LEU A  63 " --> pdb=" O   GLY A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 77
      removed outlier: 4.026A  pdb=" N   GLY A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 188 through 195
      removed outlier: 3.640A  pdb=" N   SER A 195 " --> pdb=" O   ASP A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 200 through 212
    Processing helix  chain 'A' and resid 222 through 231
      removed outlier: 4.068A  pdb=" N   ASP A 229 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU A 230 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 249
    Processing helix  chain 'A' and resid 251 through 285
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 364 through 366
      No H-bonds generated for 'chain 'A' and resid 364 through 366'
    Processing helix  chain 'A' and resid 393 through 396
    Processing helix  chain 'A' and resid 397 through 408
    Processing helix  chain 'A' and resid 417 through 445
    Processing helix  chain 'A' and resid 448 through 464
      removed outlier: 3.728A  pdb=" N   VAL A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR A 461 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 487
      removed outlier: 4.322A  pdb=" N   CYS A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   THR A 476 " --> pdb=" O   MET A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 501
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'A' and resid 566 through 577
      removed outlier: 3.567A  pdb=" N   GLY A 577 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 656
    Processing helix  chain 'A' and resid 667 through 677
    Processing helix  chain 'A' and resid 695 through 700
      removed outlier: 3.577A  pdb=" N   GLN A 700 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 709
      removed outlier: 3.702A  pdb=" N   VAL A 707 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 737
      removed outlier: 3.519A  pdb=" N   VAL A 730 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 759
    Processing helix  chain 'A' and resid 822 through 832
    Processing helix  chain 'A' and resid 835 through 842
    Processing helix  chain 'A' and resid 850 through 864
    Processing helix  chain 'A' and resid 874 through 876
      No H-bonds generated for 'chain 'A' and resid 874 through 876'
    Processing helix  chain 'A' and resid 877 through 884
    Processing helix  chain 'A' and resid 909 through 949
      removed outlier: 3.576A  pdb=" N   MET A 913 " --> pdb=" O   GLU A 909 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE A 949 " --> pdb=" O   ILE A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 963
    Processing helix  chain 'A' and resid 963 through 974
    Processing helix  chain 'A' and resid 993 through 1020
      removed outlier: 3.506A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1061
      removed outlier: 3.787A  pdb=" N   PHE A1051 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER A1061 " --> pdb=" O   ALA A1057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1072
    Processing helix  chain 'A' and resid 1073 through 1093
    Processing helix  chain 'A' and resid 1108 through 1145
      Proline residue:  A1138  - end of helix
    Processing helix  chain 'A' and resid 1152 through 1164
    Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 79
      removed outlier: 3.655A  pdb=" N   GLU A  91 " --> pdb=" O   ARG A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109
      removed outlier: 5.164A  pdb=" N   ARG A 159 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 303
      removed outlier: 4.539A  pdb=" N   CYS A 291 " --> pdb=" O   VAL A 314 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   CYS A 312 " --> pdb=" O   CYS A 293 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   VAL A 386 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU A 387 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ASP A 325 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 320 through 321
      removed outlier: 6.701A  pdb=" N   MET A 334 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ALA A 378 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLU A 332 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 490
      removed outlier: 6.871A  pdb=" N   VAL A 868 " --> pdb=" O   VAL A 886 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   ILE A 888 " --> pdb=" O   VAL A 868 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   MET A 870 " --> pdb=" O   ILE A 888 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ALA A 741 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 8.427A  pdb=" N   PHE A 846 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   MET A 743 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   THR A 844 " --> pdb=" O   ARG A 816 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   LEU A 818 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 5.593A  pdb=" N   PHE A 846 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LEU A 820 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   SER A 821 " --> pdb=" O   VAL A 771 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   ALA A 773 " --> pdb=" O   SER A 821 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   LEU A 768 " --> pdb=" O   MET A 789 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER A 783 " --> pdb=" O   THR A 774 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 524
      removed outlier: 6.838A  pdb=" N   VAL A 718 " --> pdb=" O   MET A 521 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   VAL A 523 " --> pdb=" O   LEU A 716 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU A 716 " --> pdb=" O   VAL A 523 " (cutoff:3.500A)
      removed outlier: 5.440A  pdb=" N   LEU A 713 " --> pdb=" O   SER A 687 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   SER A 687 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   SER A 633 " --> pdb=" O   ARG A 622 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   ARG A 622 " --> pdb=" O   SER A 633 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL A 635 " --> pdb=" O   LEU A 620 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER A 588 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527
      removed outlier: 3.768A  pdb=" N   ALA A 530 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 559

    467 hydrogen bonds defined for protein.
    1317 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: 3.12

  Time building geometry restraints manager: 3.46 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1975
        1.33 -     1.45: 1232
        1.45 -     1.57: 4560
        1.57 -     1.69: 12
        1.69 -     1.81: 72
  Bond restraints: 7851
  Sorted by residual:
  bond pdb=" C31 PC1 A1206 "
       pdb=" O31 PC1 A1206 "
    ideal  model  delta    sigma   weight residual
    1.330  1.456 -0.126 2.00e-02 2.50e+03 4.00e+01
  bond pdb=" C21 PC1 A1210 "
       pdb=" O21 PC1 A1210 "
    ideal  model  delta    sigma   weight residual
    1.331  1.454 -0.123 2.00e-02 2.50e+03 3.80e+01
  bond pdb=" C21 PC1 A1206 "
       pdb=" O21 PC1 A1206 "
    ideal  model  delta    sigma   weight residual
    1.331  1.452 -0.121 2.00e-02 2.50e+03 3.66e+01
  bond pdb=" F2  ALF A1201 "
       pdb="AL   ALF A1201 "
    ideal  model  delta    sigma   weight residual
    1.685  1.791 -0.106 2.00e-02 2.50e+03 2.81e+01
  bond pdb=" CAY Y01 A1211 "
       pdb=" OAW Y01 A1211 "
    ideal  model  delta    sigma   weight residual
    1.332  1.412 -0.080 2.00e-02 2.50e+03 1.59e+01
  ... (remaining 7846 not shown)

  Histogram of bond angle deviations from ideal:
       87.16 -   105.12: 231
      105.12 -   123.09: 10062
      123.09 -   141.06: 416
      141.06 -   159.03: 0
      159.03 -   177.00: 2
  Bond angle restraints: 10711
  Sorted by residual:
  angle pdb=" F1  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F2  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     108.68  177.00  -68.32 3.00e+00 1.11e-01 5.19e+02
  angle pdb=" F3  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F4  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     109.63  173.73  -64.10 3.00e+00 1.11e-01 4.57e+02
  angle pdb=" F2  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F3  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     109.59   87.56   22.03 3.00e+00 1.11e-01 5.39e+01
  angle pdb=" F1  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F4  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     109.02   87.16   21.86 3.00e+00 1.11e-01 5.31e+01
  angle pdb=" F1  ALF A1201 "
        pdb="AL   ALF A1201 "
        pdb=" F3  ALF A1201 "
      ideal   model   delta    sigma   weight residual
     109.69   89.85   19.84 3.00e+00 1.11e-01 4.37e+01
  ... (remaining 10706 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 4322
       17.81 -    35.62: 306
       35.62 -    53.43: 49
       53.43 -    71.24: 11
       71.24 -    89.05: 6
  Dihedral angle restraints: 4694
    sinusoidal: 1720
      harmonic: 2974
  Sorted by residual:
  dihedral pdb=" CA  PRO A1026 "
           pdb=" C   PRO A1026 "
           pdb=" N   LEU A1027 "
           pdb=" CA  LEU A1027 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.82  -22.18     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  PHE A 507 "
           pdb=" C   PHE A 507 "
           pdb=" N   ASP A 508 "
           pdb=" CA  ASP A 508 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.14   19.86     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  TYR A 251 "
           pdb=" C   TYR A 251 "
           pdb=" N   TYR A 252 "
           pdb=" CA  TYR A 252 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.27  -18.73     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 4691 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1129
       0.076 -    0.151: 155
       0.151 -    0.227: 13
       0.227 -    0.302: 2
       0.302 -    0.378: 7
  Chirality restraints: 1306
  Sorted by residual:
  chirality pdb=" CBG Y01 A1211 "
            pdb=" CAQ Y01 A1211 "
            pdb=" CBD Y01 A1211 "
            pdb=" CBI Y01 A1211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CBG Y01 A1204 "
            pdb=" CAQ Y01 A1204 "
            pdb=" CBD Y01 A1204 "
            pdb=" CBI Y01 A1204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.37 2.00e-01 2.50e+01 3.50e+00
  chirality pdb=" CBG Y01 A1205 "
            pdb=" CAQ Y01 A1205 "
            pdb=" CBD Y01 A1205 "
            pdb=" CBI Y01 A1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.70    0.37 2.00e-01 2.50e+01 3.37e+00
  ... (remaining 1303 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 202 "    0.011 2.00e-02 2.50e+03   2.15e-02 4.61e+00
        pdb=" CD  GLN A 202 "   -0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 202 "    0.014 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 202 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 164 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.80e+00
        pdb=" CD  GLN A 164 "   -0.034 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 164 "    0.013 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 164 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A1135 "    0.010 2.00e-02 2.50e+03   1.94e-02 3.77e+00
        pdb=" CD  GLN A1135 "   -0.034 2.00e-02 2.50e+03
        pdb=" OE1 GLN A1135 "    0.013 2.00e-02 2.50e+03
        pdb=" NE2 GLN A1135 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 45
        2.56 -     3.14: 5922
        3.14 -     3.73: 12096
        3.73 -     4.31: 17269
        4.31 -     4.90: 28956
  Nonbonded interactions: 64288
  Sorted by model distance:
  nonbonded pdb=" F2  ALF A1201 "
            pdb="MG    MG A1202 "
     model   vdw
     1.971 2.120
  nonbonded pdb=" OD2 ASP A 458 "
            pdb=" O   HOH A1301 "
     model   vdw
     2.023 2.440
  nonbonded pdb=" OD2 ASP A 508 "
            pdb="MG    MG A1202 "
     model   vdw
     2.105 2.170
  nonbonded pdb=" O   THR A 510 "
            pdb="MG    MG A1202 "
     model   vdw
     2.211 2.170
  nonbonded pdb=" N1  SPM A1203 "
            pdb=" O   HOH A1302 "
     model   vdw
     2.234 2.520
  ... (remaining 64283 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          6.320
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     24.790
  Find NCS groups from input model:        0.220
  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:             0.010
  Load rotamer database and sin/cos tables:12.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
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   0.126   7851  Z= 0.468
  Angle     :  1.345  68.320  10711  Z= 0.523
  Chirality :  0.059   0.378   1306
  Planarity :  0.006   0.043   1335
  Dihedral  : 13.103  89.046   2772
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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: -0.87 (0.24), residues: 1016
  helix: -0.20 (0.21), residues: 484
  sheet: -0.59 (0.38), residues: 163
  loop : -0.87 (0.31), residues: 369

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 1.2036
  time to fit residues: 101.1676
Evaluate side-chains
  49 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.816 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1620
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    0.2980
   chunk 53 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 94 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 748 ASN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7851  Z= 0.184
  Angle     :  0.841  31.944  10711  Z= 0.342
  Chirality :  0.040   0.137   1306
  Planarity :  0.005   0.051   1335
  Dihedral  :  7.836  59.143   1209
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer Outliers :  0.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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:  0.79 (0.26), residues: 1016
  helix:  1.28 (0.23), residues: 488
  sheet: -0.20 (0.38), residues: 169
  loop :  0.01 (0.34), residues: 359

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 0
  residues processed: 58
  average time/residue: 0.9278
  time to fit residues: 58.8466
Evaluate side-chains
  51 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.886 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1970
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 94 optimal weight:    0.7980
   chunk 102 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 179 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7851  Z= 0.249
  Angle     :  0.844  30.721  10711  Z= 0.344
  Chirality :  0.041   0.135   1306
  Planarity :  0.005   0.044   1335
  Dihedral  :  7.387  57.667   1209
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer Outliers :  1.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.27), residues: 1016
  helix:  1.75 (0.23), residues: 487
  sheet:  0.03 (0.38), residues: 170
  loop :  0.22 (0.35), residues: 359

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.924 
Fit side-chains
  outliers start: 13
  outliers final: 4
  residues processed: 61
  average time/residue: 0.9345
  time to fit residues: 62.4970
Evaluate side-chains
  50 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.884 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 4
  residues processed: 0
  time to fit residues: 1.1974
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 49 optimal weight:   40.0000
   chunk 10 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 GLN
A 179 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7851  Z= 0.208
  Angle     :  0.824  30.532  10711  Z= 0.330
  Chirality :  0.040   0.137   1306
  Planarity :  0.004   0.045   1335
  Dihedral  :  7.044  58.861   1209
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer Outliers :  2.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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:  1.62 (0.27), residues: 1016
  helix:  2.04 (0.23), residues: 486
  sheet:  0.16 (0.37), residues: 175
  loop :  0.32 (0.36), residues: 355

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 8
  residues processed: 54
  average time/residue: 0.8809
  time to fit residues: 52.3448
Evaluate side-chains
  50 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.833 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 5
  residues processed: 3
  average time/residue: 0.1102
  time to fit residues: 1.6834
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:   50.0000
   chunk 1 optimal weight:   20.0000
   chunk 74 optimal weight:    0.0980
   chunk 41 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 90 optimal weight:    0.3980
   chunk 25 optimal weight:    0.1980
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 179 GLN
A1122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7851  Z= 0.141
  Angle     :  0.803  29.806  10711  Z= 0.316
  Chirality :  0.039   0.134   1306
  Planarity :  0.004   0.045   1335
  Dihedral  :  6.402  56.789   1209
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer Outliers :  1.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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 (0.27), residues: 1016
  helix:  2.34 (0.23), residues: 487
  sheet:  0.35 (0.38), residues: 174
  loop :  0.43 (0.35), residues: 355

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 4
  residues processed: 61
  average time/residue: 0.9250
  time to fit residues: 61.8201
Evaluate side-chains
  47 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.961 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 0.1488
  time to fit residues: 1.4011
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 59 optimal weight:   30.0000
   chunk 24 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:   20.0000
   chunk 8 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 97 optimal weight:    0.5980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7851  Z= 0.238
  Angle     :  0.831  31.257  10711  Z= 0.333
  Chirality :  0.041   0.135   1306
  Planarity :  0.004   0.044   1335
  Dihedral  :  6.585  56.763   1209
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer Outliers :  1.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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:  1.98 (0.27), residues: 1016
  helix:  2.33 (0.23), residues: 486
  sheet:  0.38 (0.38), residues: 175
  loop :  0.47 (0.36), residues: 355

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.888 
Fit side-chains
  outliers start: 12
  outliers final: 5
  residues processed: 57
  average time/residue: 0.8458
  time to fit residues: 53.2017
Evaluate side-chains
  48 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.813 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 3
  residues processed: 2
  average time/residue: 0.6375
  time to fit residues: 2.5879
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 46 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7851  Z= 0.221
  Angle     :  0.830  30.975  10711  Z= 0.330
  Chirality :  0.040   0.134   1306
  Planarity :  0.004   0.043   1335
  Dihedral  :  6.617  57.171   1209
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer Outliers :  1.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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:  2.01 (0.27), residues: 1016
  helix:  2.33 (0.23), residues: 487
  sheet:  0.36 (0.37), residues: 180
  loop :  0.56 (0.36), residues: 349

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.934 
Fit side-chains
  outliers start: 10
  outliers final: 7
  residues processed: 53
  average time/residue: 0.8281
  time to fit residues: 48.6826
Evaluate side-chains
  50 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.883 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 5
  residues processed: 2
  average time/residue: 0.5860
  time to fit residues: 2.4951
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:   30.0000
   chunk 9 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7851  Z= 0.204
  Angle     :  0.825  30.726  10711  Z= 0.328
  Chirality :  0.040   0.123   1306
  Planarity :  0.004   0.042   1335
  Dihedral  :  6.516  58.001   1209
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer Outliers :  1.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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:  2.06 (0.27), residues: 1016
  helix:  2.37 (0.23), residues: 488
  sheet:  0.43 (0.37), residues: 179
  loop :  0.56 (0.36), residues: 349

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.912 
Fit side-chains
  outliers start: 11
  outliers final: 6
  residues processed: 55
  average time/residue: 0.9862
  time to fit residues: 62.8966
Evaluate side-chains
  48 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.923 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 5
  residues processed: 1
  average time/residue: 0.1423
  time to fit residues: 1.3851
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 88 optimal weight:    0.5980
   chunk 93 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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: 0.8323
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7851  Z= 0.187
  Angle     :  0.824  30.559  10711  Z= 0.327
  Chirality :  0.040   0.127   1306
  Planarity :  0.004   0.042   1335
  Dihedral  :  6.421  58.382   1209
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer Outliers :  0.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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:  2.13 (0.27), residues: 1016
  helix:  2.41 (0.23), residues: 488
  sheet:  0.56 (0.37), residues: 178
  loop :  0.55 (0.36), residues: 350

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.926 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 50
  average time/residue: 0.8970
  time to fit residues: 49.5396
Evaluate side-chains
  47 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.826 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 1
  average time/residue: 0.1313
  time to fit residues: 1.3838
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0070
   chunk 82 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7851  Z= 0.180
  Angle     :  0.823  30.447  10711  Z= 0.327
  Chirality :  0.040   0.125   1306
  Planarity :  0.004   0.042   1335
  Dihedral  :  6.356  59.032   1209
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer Outliers :  0.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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:  2.19 (0.27), residues: 1016
  helix:  2.45 (0.23), residues: 488
  sheet:  0.62 (0.38), residues: 178
  loop :  0.57 (0.36), residues: 350

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.923 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 49
  average time/residue: 0.8957
  time to fit residues: 48.6309
Evaluate side-chains
  47 residues out of total 881 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.942 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 0.1263
  time to fit residues: 1.4033
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    0.0040
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0970
   chunk 4 optimal weight:    3.9990
   chunk 59 optimal weight:   20.0000
   overall best weight:    0.9392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.108505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.073505 restraints weight = 12575.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.14
r_work: 0.2865 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7851  Z= 0.225
  Angle     :  0.832  30.821  10711  Z= 0.333
  Chirality :  0.041   0.149   1306
  Planarity :  0.004   0.042   1335
  Dihedral  :  6.393  59.131   1209
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer Outliers :  0.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.29 %
    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:  2.13 (0.27), residues: 1016
  helix:  2.36 (0.23), residues: 490
  sheet:  0.70 (0.38), residues: 175
  loop :  0.54 (0.36), residues: 351

===============================================================================
Job complete
usr+sys time: 2246.71 seconds
wall clock time: 40 minutes 54.00 seconds (2454.00 seconds total)