Starting phenix.real_space_refine
on Thu Feb 13 09:47:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n72_24217/02_2025/7n72_24217_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n72_24217/02_2025/7n72_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/cci-nas-00/data/ceres_data/7n72_24217/02_2025/7n72_24217.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n72_24217/02_2025/7n72_24217.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n72_24217/02_2025/7n72_24217_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n72_24217/02_2025/7n72_24217_trim.cif"
  }
  resolution = 2.5
  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=   0.001 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. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7705
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1030, 7475
          Classifications: {'peptide': 1030}
          Incomplete info: {'truncation_to_alanine': 135}
          Link IDs: {'PCIS': 3, 'PTRANS': 68, 'TRANS': 958}
          Chain breaks: 6
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 505
          Unresolved non-hydrogen angles: 652
          Unresolved non-hydrogen dihedrals: 427
          Unresolved non-hydrogen chiralities: 45
          Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 6, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 17}
          Unresolved non-hydrogen planarities: 290
    Chain: "A"
      Number of atoms: 230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 230
          Unusual residues: {' MG': 1, 'ALF': 1, 'LMT': 3, 'PC1': 2, 'SPM': 1, 'Y01': 3}
          Classifications: {'undetermined': 11, 'water': 5}
          Link IDs: {None: 15}
          Unresolved non-hydrogen bonds: 118
          Unresolved non-hydrogen angles: 159
          Unresolved non-hydrogen dihedrals: 182
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'PC1:plan-2': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 5.12, per 1000 atoms: 0.66
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 1.0 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: 1.00
  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: 3.16

  Time building geometry restraints manager: 2.52 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:
        0.00 -    13.66: 10702
       13.66 -    27.33: 7
       27.33 -    40.99: 0
       40.99 -    54.66: 0
       54.66 -    68.32: 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: 4512
       17.81 -    35.62: 314
       35.62 -    53.43: 55
       53.43 -    71.24: 13
       71.24 -    89.05: 7
  Dihedral angle restraints: 4901
    sinusoidal: 1927
      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 4898 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 3.040
  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 3.120
  ... (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:             2.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     22.390
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.160
-------------------------------------------------------------------------------
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  : 13.129  89.046   2979
  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 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1166 
 HIS   0.014   0.002   HIS A  84 
 PHE   0.011   0.002   PHE A1154 
 TYR   0.016   0.002   TYR A 931 
 ARG   0.030   0.002   ARG A 444 

*********************** 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 to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.6989 (mtt) cc_final: 0.5785 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 1.2548
  time to fit residues: 105.4718
Evaluate side-chains
  49 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    8.9990
   chunk 52 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 49 optimal weight:   40.0000
   chunk 60 optimal weight:    0.8980
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.110337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.074970 restraints weight = 12654.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.14
r_work: 0.2871 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1232

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= 0.192
  Angle     :  0.846  31.084  10711  Z= 0.347
  Chirality :  0.041   0.136   1306
  Planarity :  0.005   0.056   1335
  Dihedral  :  8.708  80.049   1416
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  7.37 %
    Favored  : 91.69 %
  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:  0.74 (0.26), residues: 1016
  helix:  1.24 (0.23), residues: 486
  sheet: -0.23 (0.38), residues: 169
  loop :  0.00 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 253 
 HIS   0.004   0.001   HIS A 831 
 PHE   0.012   0.001   PHE A1154 
 TYR   0.017   0.001   TYR A 931 
 ARG   0.010   0.000   ARG A 366 

*********************** 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
  59 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 TYR cc_start: 0.7881 (m-80) cc_final: 0.7222 (m-80)
REVERT: A  421 MET cc_start: 0.6959 (mtt) cc_final: 0.5735 (tpt)
REVERT: A  521 MET cc_start: 0.7977 (mmm) cc_final: 0.7659 (mmm)
REVERT: A  955 ASP cc_start: 0.8963 (m-30) cc_final: 0.8627 (m-30)
  outliers start: 7
  outliers final: 1
  residues processed: 57
  average time/residue: 0.9450
  time to fit residues: 58.8518
Evaluate side-chains
  51 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.108969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.073460 restraints weight = 12848.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 2.14
r_work: 0.2842 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1470

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= 0.257
  Angle     :  0.847  31.055  10711  Z= 0.345
  Chirality :  0.042   0.134   1306
  Planarity :  0.005   0.044   1335
  Dihedral  :  8.189  75.881   1416
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  7.77 %
    Favored  : 90.88 %
  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:  1.27 (0.27), residues: 1016
  helix:  1.73 (0.23), residues: 485
  sheet:  0.09 (0.38), residues: 165
  loop :  0.12 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 775 
 PHE   0.012   0.001   PHE A1154 
 TYR   0.017   0.001   TYR A 931 
 ARG   0.005   0.000   ARG A 366 

*********************** 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
  61 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A   84 HIS cc_start: 0.7960 (m90) cc_final: 0.7581 (m90)
REVERT: A  379 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7896 (mmp-170)
REVERT: A  421 MET cc_start: 0.7086 (mtt) cc_final: 0.5812 (tpt)
REVERT: A  521 MET cc_start: 0.8144 (mmm) cc_final: 0.7684 (mmm)
  outliers start: 10
  outliers final: 4
  residues processed: 57
  average time/residue: 0.8430
  time to fit residues: 52.9192
Evaluate side-chains
  50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0170
   chunk 14 optimal weight:    0.0870
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.110258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.074995 restraints weight = 12696.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.14
r_work: 0.2876 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1696

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= 0.169
  Angle     :  0.811  30.292  10711  Z= 0.325
  Chirality :  0.040   0.140   1306
  Planarity :  0.004   0.045   1335
  Dihedral  :  7.741  78.374   1416
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  9.65 %
    Favored  : 89.01 %
  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:  1.55 (0.27), residues: 1016
  helix:  2.04 (0.23), residues: 487
  sheet: -0.04 (0.37), residues: 175
  loop :  0.29 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 775 
 PHE   0.011   0.001   PHE A1154 
 TYR   0.015   0.001   TYR A 931 
 ARG   0.003   0.000   ARG A 366 

*********************** 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
  64 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 HIS cc_start: 0.7909 (m90) cc_final: 0.7563 (m90)
REVERT: A  178 TYR cc_start: 0.7794 (m-80) cc_final: 0.7170 (m-80)
REVERT: A  379 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7866 (mmp-170)
REVERT: A  385 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.7455 (p90)
REVERT: A  421 MET cc_start: 0.7024 (mtt) cc_final: 0.5719 (tpt)
REVERT: A  521 MET cc_start: 0.8171 (mmm) cc_final: 0.7716 (mmm)
REVERT: A 1160 GLU cc_start: 0.8218 (pt0) cc_final: 0.7735 (pp20)
  outliers start: 10
  outliers final: 3
  residues processed: 61
  average time/residue: 0.8978
  time to fit residues: 59.8900
Evaluate side-chains
  53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 68 optimal weight:    0.0770
   chunk 80 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 102 optimal weight:    0.7980
   chunk 67 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 53 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 748 ASN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.110247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.075187 restraints weight = 12710.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.14
r_work: 0.2881 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7851  Z= 0.165
  Angle     :  0.812  30.359  10711  Z= 0.322
  Chirality :  0.040   0.137   1306
  Planarity :  0.004   0.045   1335
  Dihedral  :  7.444  77.037   1416
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 10.32 %
    Favored  : 88.20 %
  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:  1.78 (0.27), residues: 1016
  helix:  2.26 (0.23), residues: 487
  sheet: -0.01 (0.37), residues: 180
  loop :  0.42 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 253 
 HIS   0.003   0.000   HIS A 775 
 PHE   0.011   0.001   PHE A1154 
 TYR   0.014   0.001   TYR A 931 
 ARG   0.003   0.000   ARG A 366 

*********************** 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
  62 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 HIS cc_start: 0.7870 (m90) cc_final: 0.7552 (m90)
REVERT: A  174 GLN cc_start: 0.8314 (tt0) cc_final: 0.7720 (tm-30)
REVERT: A  178 TYR cc_start: 0.7667 (m-80) cc_final: 0.7109 (m-80)
REVERT: A  385 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.7851 (p90)
REVERT: A  421 MET cc_start: 0.6974 (mtt) cc_final: 0.5691 (tpt)
REVERT: A  521 MET cc_start: 0.8221 (mmm) cc_final: 0.7727 (mmm)
REVERT: A 1160 GLU cc_start: 0.8180 (pt0) cc_final: 0.7738 (pp20)
  outliers start: 11
  outliers final: 5
  residues processed: 59
  average time/residue: 0.9320
  time to fit residues: 60.1573
Evaluate side-chains
  53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 70 optimal weight:    0.1980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.109128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.073905 restraints weight = 12732.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 2.14
r_work: 0.2886 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7851  Z= 0.219
  Angle     :  0.828  30.961  10711  Z= 0.331
  Chirality :  0.041   0.130   1306
  Planarity :  0.004   0.044   1335
  Dihedral  :  7.478  75.248   1416
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.99 %
    Favored  : 87.80 %
  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:  1.82 (0.27), residues: 1016
  helix:  2.26 (0.23), residues: 487
  sheet:  0.10 (0.37), residues: 178
  loop :  0.42 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 775 
 PHE   0.011   0.001   PHE A1154 
 TYR   0.015   0.001   TYR A 931 
 ARG   0.002   0.000   ARG A 816 

*********************** 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
  62 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A   84 HIS cc_start: 0.7907 (m90) cc_final: 0.7611 (m90)
REVERT: A  174 GLN cc_start: 0.8262 (tt0) cc_final: 0.7571 (tm-30)
REVERT: A  178 TYR cc_start: 0.7795 (m-80) cc_final: 0.7114 (m-80)
REVERT: A  385 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.7891 (p90)
REVERT: A  521 MET cc_start: 0.8242 (mmm) cc_final: 0.7706 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 60
  average time/residue: 0.7781
  time to fit residues: 52.1627
Evaluate side-chains
  53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0000
   chunk 34 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6784

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.109716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.074535 restraints weight = 12789.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.15
r_work: 0.2869 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7851  Z= 0.184
  Angle     :  0.819  30.538  10711  Z= 0.325
  Chirality :  0.040   0.131   1306
  Planarity :  0.004   0.044   1335
  Dihedral  :  7.310  75.504   1416
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.53 %
    Favored  : 87.27 %
  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:  1.95 (0.27), residues: 1016
  helix:  2.36 (0.23), residues: 488
  sheet:  0.10 (0.37), residues: 180
  loop :  0.54 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 253 
 HIS   0.003   0.000   HIS A 775 
 PHE   0.034   0.001   PHE A1123 
 TYR   0.015   0.001   TYR A 931 
 ARG   0.002   0.000   ARG A 816 

*********************** 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
  59 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A   84 HIS cc_start: 0.7935 (m90) cc_final: 0.7645 (m90)
REVERT: A  174 GLN cc_start: 0.8266 (tt0) cc_final: 0.7589 (tm-30)
REVERT: A  178 TYR cc_start: 0.7849 (m-80) cc_final: 0.7235 (m-80)
REVERT: A  385 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.7504 (p90)
REVERT: A  421 MET cc_start: 0.7091 (mtt) cc_final: 0.5845 (tpt)
REVERT: A  521 MET cc_start: 0.8232 (mmm) cc_final: 0.7834 (mmm)
REVERT: A 1160 GLU cc_start: 0.8171 (pt0) cc_final: 0.7756 (pp20)
  outliers start: 9
  outliers final: 4
  residues processed: 56
  average time/residue: 0.8513
  time to fit residues: 52.5290
Evaluate side-chains
  51 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 8 optimal weight:    0.4980
   chunk 97 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0770
   chunk 48 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.4542

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.107549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.072011 restraints weight = 12863.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 2.16
r_work: 0.2822 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2693 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7851  Z= 0.318
  Angle     :  0.866  31.789  10711  Z= 0.352
  Chirality :  0.042   0.141   1306
  Planarity :  0.004   0.044   1335
  Dihedral  :  7.557  75.369   1416
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 12.33 %
    Favored  : 86.73 %
  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:  1.81 (0.27), residues: 1016
  helix:  2.15 (0.23), residues: 488
  sheet:  0.31 (0.39), residues: 171
  loop :  0.44 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 253 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.030   0.002   PHE A1123 
 TYR   0.017   0.002   TYR A 931 
 ARG   0.003   0.000   ARG A 816 

*********************** 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
  56 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   84 HIS cc_start: 0.7967 (m90) cc_final: 0.7671 (m90)
REVERT: A  178 TYR cc_start: 0.7983 (m-80) cc_final: 0.7505 (m-80)
REVERT: A  385 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.7572 (p90)
REVERT: A  521 MET cc_start: 0.8302 (mmm) cc_final: 0.7794 (mmm)
REVERT: A  541 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7723 (pp)
  outliers start: 7
  outliers final: 3
  residues processed: 52
  average time/residue: 0.8601
  time to fit residues: 49.4497
Evaluate side-chains
  50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0370
   chunk 71 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0770
   chunk 64 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 174 GLN
A 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.109821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.074805 restraints weight = 13022.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.17
r_work: 0.2875 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7851  Z= 0.157
  Angle     :  0.819  30.002  10711  Z= 0.325
  Chirality :  0.040   0.126   1306
  Planarity :  0.004   0.044   1335
  Dihedral  :  7.186  77.727   1416
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 12.20 %
    Favored  : 86.73 %
  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:  2.37 (0.23), residues: 489
  sheet:  0.30 (0.38), residues: 178
  loop :  0.52 (0.36), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 253 
 HIS   0.003   0.000   HIS A 775 
 PHE   0.031   0.001   PHE A1123 
 TYR   0.015   0.001   TYR A 931 
 ARG   0.002   0.000   ARG A 366 

*********************** 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
  59 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A   84 HIS cc_start: 0.7965 (m90) cc_final: 0.7663 (m90)
REVERT: A  178 TYR cc_start: 0.7736 (m-80) cc_final: 0.7499 (m-80)
REVERT: A  385 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.7534 (p90)
REVERT: A  421 MET cc_start: 0.7126 (mtt) cc_final: 0.5748 (tpt)
REVERT: A  521 MET cc_start: 0.8262 (mmm) cc_final: 0.7864 (mmm)
REVERT: A  541 LEU cc_start: 0.8276 (mp) cc_final: 0.7765 (pp)
REVERT: A 1160 GLU cc_start: 0.8150 (pt0) cc_final: 0.7747 (pp20)
  outliers start: 8
  outliers final: 4
  residues processed: 58
  average time/residue: 0.8419
  time to fit residues: 54.1941
Evaluate side-chains
  53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 85 optimal weight:    0.0870
   chunk 35 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   chunk 68 optimal weight:    4.9990
   chunk 54 optimal weight:   20.0000
   chunk 75 optimal weight:    0.1980
   chunk 89 optimal weight:    0.0470
   overall best weight:    0.8058

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.108489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.073543 restraints weight = 12789.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.17
r_work: 0.2840 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2146

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= 0.208
  Angle     :  0.832  31.029  10711  Z= 0.332
  Chirality :  0.040   0.126   1306
  Planarity :  0.004   0.043   1335
  Dihedral  :  7.207  79.638   1416
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 12.33 %
    Favored  : 86.86 %
  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:  2.04 (0.27), residues: 1016
  helix:  2.36 (0.23), residues: 489
  sheet:  0.39 (0.38), residues: 178
  loop :  0.53 (0.36), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 253 
 HIS   0.002   0.000   HIS A 775 
 PHE   0.030   0.001   PHE A1123 
 TYR   0.014   0.001   TYR A 931 
 ARG   0.001   0.000   ARG A 816 

********************** 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
  53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A   84 HIS cc_start: 0.7973 (m90) cc_final: 0.7676 (m90)
REVERT: A  178 TYR cc_start: 0.7673 (m-80) cc_final: 0.7372 (m-80)
REVERT: A  421 MET cc_start: 0.6969 (mtt) cc_final: 0.5697 (tpt)
REVERT: A  521 MET cc_start: 0.8216 (mmm) cc_final: 0.7740 (mmm)
REVERT: A  541 LEU cc_start: 0.8104 (mt) cc_final: 0.7671 (pp)
  outliers start: 6
  outliers final: 5
  residues processed: 52
  average time/residue: 0.8020
  time to fit residues: 46.3839
Evaluate side-chains
  52 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 66 optimal weight:    0.4980
   chunk 55 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 52 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.108653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.073811 restraints weight = 12718.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.15
r_work: 0.2846 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
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      :  0.003   0.028   7851  Z= 0.195
  Angle     :  0.821  30.799  10711  Z= 0.327
  Chirality :  0.040   0.152   1306
  Planarity :  0.004   0.043   1335
  Dihedral  :  7.168  81.587   1416
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 12.20 %
    Favored  : 87.00 %
  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:  2.10 (0.27), residues: 1016
  helix:  2.40 (0.23), residues: 489
  sheet:  0.43 (0.38), residues: 178
  loop :  0.57 (0.36), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 775 
 PHE   0.030   0.001   PHE A1123 
 TYR   0.015   0.001   TYR A 931 
 ARG   0.002   0.000   ARG A 816 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6132.15 seconds
wall clock time: 108 minutes 50.62 seconds (6530.62 seconds total)