Starting phenix.real_space_refine
on Sun Oct 13 10:21:30 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umf_42378/10_2024/8umf_42378.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umf_42378/10_2024/8umf_42378.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umf_42378/10_2024/8umf_42378.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umf_42378/10_2024/8umf_42378.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umf_42378/10_2024/8umf_42378.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umf_42378/10_2024/8umf_42378.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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: 6
    Type Number    sf(0)   Gaussians
     P     172      5.49       5
     Mg      7      5.21       5
     S      37      5.16       5
     C    8725      2.51       5
     N    2621      2.21       5
     O    3242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib"
  Total number of atoms: 14804
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 11159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1376, 11159
          Classifications: {'peptide': 1376}
          Link IDs: {'PTRANS': 38, 'TRANS': 1337}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2568
          Classifications: {'RNA': 121}
          Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 58, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 15, 'rna3p': 105}
    Chain: "C"
      Number of atoms: 372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 372
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "D"
      Number of atoms: 395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 395
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "E"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 303
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 10.55, per 1000 atoms: 0.71
  Number of scatterers: 14804
  At special positions: 0
  Unit cell: (91.53, 113.4, 139.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      37     16.00
     P     172     15.00
     Mg      7     11.99
     O    3242      8.00
     N    2621      7.00
     C    8725      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=0, symmetry=0
  Time building additional restraints: 3.98
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2628

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 10 sheets defined
      55.3% alpha, 10.3% beta
      65 base pairs and 119 stacking pairs defined.
    Time for finding SS restraints: 7.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 82
    Processing helix  chain 'A' and resid 86 through 98
    Processing helix  chain 'A' and resid 111 through 115
      removed outlier: 3.518A  pdb=" N   LEU A 114 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 123
      removed outlier: 3.775A  pdb=" N   PHE A 121 " --> pdb=" O   GLU A 118 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS A 123 " --> pdb=" O   GLY A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 148
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 167 through 178
    Processing helix  chain 'A' and resid 181 through 200
      removed outlier: 3.632A  pdb=" N   SER A 197 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   MET A 198 " --> pdb=" O   ASP A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 220
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 226 through 233
      removed outlier: 3.651A  pdb=" N   GLU A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA A 232 " --> pdb=" O   PRO A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 248
    Processing helix  chain 'A' and resid 250 through 259
    Processing helix  chain 'A' and resid 260 through 266
      removed outlier: 3.634A  pdb=" N   ASN A 265 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 282
    Processing helix  chain 'A' and resid 290 through 303
      removed outlier: 3.541A  pdb=" N   ASN A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 314
    Processing helix  chain 'A' and resid 340 through 348
    Processing helix  chain 'A' and resid 350 through 361
      removed outlier: 3.841A  pdb=" N   ILE A 354 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
    Processing helix  chain 'A' and resid 371 through 376
    Processing helix  chain 'A' and resid 381 through 391
    Processing helix  chain 'A' and resid 397 through 412
    Processing helix  chain 'A' and resid 421 through 426
    Processing helix  chain 'A' and resid 432 through 448
      removed outlier: 4.025A  pdb=" N   ILE A 436 " --> pdb=" O   ASN A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 471
    Processing helix  chain 'A' and resid 472 through 477
      removed outlier: 5.426A  pdb=" N   PHE A 475 " --> pdb=" O   GLY A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 506
      removed outlier: 3.556A  pdb=" N   ARG A 499 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 517
    Processing helix  chain 'A' and resid 526 through 541
    Processing helix  chain 'A' and resid 543 through 557
    Processing helix  chain 'A' and resid 562 through 586
    Processing helix  chain 'A' and resid 589 through 594
    Processing helix  chain 'A' and resid 598 through 610
    Processing helix  chain 'A' and resid 620 through 632
    Processing helix  chain 'A' and resid 652 through 674
    Processing helix  chain 'A' and resid 699 through 707
      removed outlier: 4.281A  pdb=" N   LYS A 705 " --> pdb=" O   ALA A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 738
      removed outlier: 3.834A  pdb=" N   SER A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 769
    Processing helix  chain 'A' and resid 774 through 776
      No H-bonds generated for 'chain 'A' and resid 774 through 776'
    Processing helix  chain 'A' and resid 782 through 788
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 800 through 809
    Processing helix  chain 'A' and resid 812 through 826
    Processing helix  chain 'A' and resid 828 through 834
    Processing helix  chain 'A' and resid 835 through 838
    Processing helix  chain 'A' and resid 839 through 849
    Processing helix  chain 'A' and resid 850 through 852
      No H-bonds generated for 'chain 'A' and resid 850 through 852'
    Processing helix  chain 'A' and resid 856 through 866
      removed outlier: 3.561A  pdb=" N   ARG A 864 " --> pdb=" O   ARG A 860 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 873
    Processing helix  chain 'A' and resid 877 through 893
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 913 through 920
    Processing helix  chain 'A' and resid 920 through 928
    Processing helix  chain 'A' and resid 929 through 932
    Processing helix  chain 'A' and resid 940 through 956
      removed outlier: 4.102A  pdb=" N   HIS A 944 " --> pdb=" O   PRO A 940 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ALA A 945 " --> pdb=" O   ILE A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 966
      removed outlier: 4.092A  pdb=" N   VAL A 964 " --> pdb=" O   ASN A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 972 through 981
      removed outlier: 3.588A  pdb=" N   ASN A 976 " --> pdb=" O   ALA A 972 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ALA A 981 " --> pdb=" O   LEU A 977 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1007
    Processing helix  chain 'A' and resid 1046 through 1052
    Processing helix  chain 'A' and resid 1074 through 1088
      removed outlier: 3.683A  pdb=" N   PHE A1086 " --> pdb=" O   LEU A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1104
    Processing helix  chain 'A' and resid 1126 through 1131
    Processing helix  chain 'A' and resid 1132 through 1135
    Processing helix  chain 'A' and resid 1156 through 1166
      removed outlier: 4.075A  pdb=" N   GLU A1160 " --> pdb=" O   PRO A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1197
      removed outlier: 3.529A  pdb=" N   LEU A1192 " --> pdb=" O   ASP A1188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1325 through 1333
    Processing helix  chain 'A' and resid 1338 through 1342
    Processing helix  chain 'A' and resid 1349 through 1361
    Processing helix  chain 'A' and resid 1368 through 1370
      No H-bonds generated for 'chain 'A' and resid 1368 through 1370'
    Processing helix  chain 'A' and resid 1392 through 1409
      removed outlier: 3.597A  pdb=" N   GLN A1409 " --> pdb=" O   VAL A1405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 903 through 912
      removed outlier: 3.906A  pdb=" N   GLU A 690 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ALA A  35 " --> pdb=" O   ASN A 989 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   ILE A 991 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   VAL A  37 " --> pdb=" O   ILE A 991 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 339
    Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521
      removed outlier: 7.110A  pdb=" N   SER A 524 " --> pdb=" O   VAL A 520 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 754 through 757
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1215 through 1218
      removed outlier: 6.411A  pdb=" N   ASN A1110 " --> pdb=" O   ILE A1014 " (cutoff:3.500A)
      removed outlier: 8.746A  pdb=" N   ILE A1014 " --> pdb=" O   ASN A1110 " (cutoff:3.500A)
      removed outlier: 13.686A  pdb=" N   SER A1112 " --> pdb=" O   GLU A1012 " (cutoff:3.500A)
      removed outlier: 18.968A  pdb=" N   GLU A1012 " --> pdb=" O   SER A1112 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   GLY A1013 " --> pdb=" O   MET A1243 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   MET A1243 " --> pdb=" O   GLY A1013 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   LEU A1241 " --> pdb=" O   PHE A1015 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   GLU A1017 " --> pdb=" O   TYR A1239 " (cutoff:3.500A)
      removed outlier: 9.609A  pdb=" N   TYR A1239 " --> pdb=" O   GLU A1017 " (cutoff:3.500A)
      removed outlier: 15.770A  pdb=" N   PHE A1019 " --> pdb=" O   ASP A1237 " (cutoff:3.500A)
      removed outlier: 20.399A  pdb=" N   ASP A1237 " --> pdb=" O   PHE A1019 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1040 through 1042
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1118
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1137 through 1141
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1266 through 1267
      removed outlier: 7.788A  pdb=" N   LEU A1266 " --> pdb=" O   LYS A1250 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   GLN A1288 " --> pdb=" O   VAL A1254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1296 through 1297
      removed outlier: 6.555A  pdb=" N   LYS A1383 " --> pdb=" O   ILE A1376 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   CYS A1387 " --> pdb=" O   GLN A1372 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   GLN A1372 " --> pdb=" O   CYS A1387 " (cutoff:3.500A)

    561 hydrogen bonds defined for protein.
    1596 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      160 hydrogen bonds
      302 hydrogen bond angles
      0 basepair planarities
      65 basepair parallelities
      119 stacking parallelities
  Total time for adding SS restraints: 11.89

  Time building geometry restraints manager: 4.42 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: 2957
        1.33 -     1.45: 4318
        1.45 -     1.57: 7754
        1.57 -     1.69: 341
        1.69 -     1.81: 57
  Bond restraints: 15427
  Sorted by residual:
  bond pdb=" C3'   C B  57 "
       pdb=" O3'   C B  57 "
    ideal  model  delta    sigma   weight residual
    1.427  1.457 -0.030 1.50e-02 4.44e+03 3.87e+00
  bond pdb=" CB  ARG A  70 "
       pdb=" CG  ARG A  70 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.049 3.00e-02 1.11e+03 2.65e+00
  bond pdb=" CB  VAL A1226 "
       pdb=" CG1 VAL A1226 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.35e+00
  bond pdb=" CG  LYS A 888 "
       pdb=" CD  LYS A 888 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.10e+00
  bond pdb=" CD  LYS A 888 "
       pdb=" CE  LYS A 888 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.02e+00
  ... (remaining 15422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 20876
        1.92 -     3.83: 624
        3.83 -     5.75: 89
        5.75 -     7.66: 22
        7.66 -     9.58: 8
  Bond angle restraints: 21619
  Sorted by residual:
  angle pdb=" C3'   C B  57 "
        pdb=" O3'   C B  57 "
        pdb=" P     U B  58 "
      ideal   model   delta    sigma   weight residual
     120.20  127.50   -7.30 1.50e+00 4.44e-01 2.37e+01
  angle pdb=" C   LYS A 679 "
        pdb=" N   ASN A 680 "
        pdb=" CA  ASN A 680 "
      ideal   model   delta    sigma   weight residual
     122.46  128.25   -5.79 1.41e+00 5.03e-01 1.69e+01
  angle pdb=" C   ASN A 766 "
        pdb=" N   TYR A 767 "
        pdb=" CA  TYR A 767 "
      ideal   model   delta    sigma   weight residual
     122.54  115.91    6.63 1.65e+00 3.67e-01 1.62e+01
  angle pdb=" N   GLU A 370 "
        pdb=" CA  GLU A 370 "
        pdb=" C   GLU A 370 "
      ideal   model   delta    sigma   weight residual
     111.02  115.62   -4.60 1.22e+00 6.72e-01 1.42e+01
  angle pdb=" N   GLN A 158 "
        pdb=" CA  GLN A 158 "
        pdb=" CB  GLN A 158 "
      ideal   model   delta    sigma   weight residual
     110.39  116.52   -6.13 1.66e+00 3.63e-01 1.36e+01
  ... (remaining 21614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.51: 8827
       35.51 -    71.02: 477
       71.02 -   106.53: 45
      106.53 -   142.03: 1
      142.03 -   177.54: 5
  Dihedral angle restraints: 9355
    sinusoidal: 5304
      harmonic: 4051
  Sorted by residual:
  dihedral pdb=" O4'   U B 101 "
           pdb=" C1'   U B 101 "
           pdb=" N1    U B 101 "
           pdb=" C2    U B 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.64  149.36     1      1.50e+01 4.44e-03 7.94e+01
  dihedral pdb=" O4'   U B 108 "
           pdb=" C1'   U B 108 "
           pdb=" N1    U B 108 "
           pdb=" C2    U B 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.54 -177.54     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B  85 "
           pdb=" C1'   U B  85 "
           pdb=" N1    U B  85 "
           pdb=" C2    U B  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   47.17 -175.17     1      1.70e+01 3.46e-03 6.63e+01
  ... (remaining 9352 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 2058
       0.057 -    0.115: 380
       0.115 -    0.172: 61
       0.172 -    0.230: 9
       0.230 -    0.287: 2
  Chirality restraints: 2510
  Sorted by residual:
  chirality pdb=" CB  THR A1381 "
            pdb=" CA  THR A1381 "
            pdb=" OG1 THR A1381 "
            pdb=" CG2 THR A1381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.26    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" C3'   C B  57 "
            pdb=" C4'   C B  57 "
            pdb=" O3'   C B  57 "
            pdb=" C2'   C B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.49   -0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CB  VAL A 575 "
            pdb=" CA  VAL A 575 "
            pdb=" CG1 VAL A 575 "
            pdb=" CG2 VAL A 575 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 2507 not shown)

  Planarity restraints: 2136
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  15 "    0.058 2.00e-02 2.50e+03   2.46e-02 1.82e+01
        pdb=" N9    G B  15 "   -0.058 2.00e-02 2.50e+03
        pdb=" C8    G B  15 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7    G B  15 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B  15 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B  15 "    0.009 2.00e-02 2.50e+03
        pdb=" O6    G B  15 "    0.013 2.00e-02 2.50e+03
        pdb=" N1    G B  15 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    G B  15 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2    G B  15 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G B  15 "   -0.012 2.00e-02 2.50e+03
        pdb=" C4    G B  15 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  99 "   -0.046 2.00e-02 2.50e+03   1.93e-02 1.12e+01
        pdb=" N9    G B  99 "    0.045 2.00e-02 2.50e+03
        pdb=" C8    G B  99 "    0.007 2.00e-02 2.50e+03
        pdb=" N7    G B  99 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G B  99 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    G B  99 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6    G B  99 "   -0.016 2.00e-02 2.50e+03
        pdb=" N1    G B  99 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    G B  99 "    0.004 2.00e-02 2.50e+03
        pdb=" N2    G B  99 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    G B  99 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G B  99 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 106 "   -0.014 2.00e-02 2.50e+03   2.92e-02 8.52e+00
        pdb=" C   GLU A 106 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLU A 106 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER A 107 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 2133 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 315
        2.65 -     3.21: 12606
        3.21 -     3.77: 26154
        3.77 -     4.34: 36347
        4.34 -     4.90: 54274
  Nonbonded interactions: 129696
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 756 "
            pdb="MG    MG A1503 "
     model   vdw
     2.087 2.170
  nonbonded pdb=" OD2 ASP A  10 "
            pdb="MG    MG A1502 "
     model   vdw
     2.102 2.170
  nonbonded pdb=" OP1  DC C  43 "
            pdb="MG    MG A1502 "
     model   vdw
     2.125 2.170
  nonbonded pdb=" OP2  DC C  43 "
            pdb="MG    MG A1501 "
     model   vdw
     2.142 2.170
  nonbonded pdb=" OG  SER A  94 "
            pdb=" OP1   A B  72 "
     model   vdw
     2.189 3.040
  ... (remaining 129691 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=0.00 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:             4.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.120
  Process input model:                     45.290
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.060
  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:13.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  15427  Z= 0.320
  Angle     :  0.802   9.576  21619  Z= 0.436
  Chirality :  0.047   0.287   2510
  Planarity :  0.005   0.044   2136
  Dihedral  : 19.052 177.543   6727
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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: -1.20 (0.21), residues: 1368
  helix: -0.80 (0.17), residues: 673
  sheet: -0.23 (0.42), residues: 155
  loop : -0.72 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 516 
 HIS   0.009   0.002   HIS A 206 
 PHE   0.022   0.002   PHE A 242 
 TYR   0.027   0.002   TYR A 819 
 ARG   0.018   0.001   ARG A 527 

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1231 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.429 
Fit side-chains
  outliers start: 0
  outliers final: 2
  residues processed: 106
  average time/residue: 1.9050
  time to fit residues: 218.7567
Evaluate side-chains
  57 residues out of total 1231 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue 1047 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.9980
   chunk 115 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 119 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 138 optimal weight:    2.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
A 604 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  15427  Z= 0.342
  Angle     :  0.625   7.285  21619  Z= 0.335
  Chirality :  0.041   0.209   2510
  Planarity :  0.004   0.038   2136
  Dihedral  : 20.558 177.778   3904
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  6.42 %
    Favored  : 92.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.11 (0.22), residues: 1368
  helix:  0.36 (0.19), residues: 680
  sheet: -0.06 (0.42), residues: 150
  loop : -0.47 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1035 
 HIS   0.006   0.001   HIS A1105 
 PHE   0.023   0.001   PHE A 160 
 TYR   0.016   0.002   TYR A 281 
 ARG   0.006   0.001   ARG A 655 

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1231 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
REVERT: A  413 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8613 (ttp-170)
REVERT: A  440 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7574 (tm-30)
  outliers start: 14
  outliers final: 5
  residues processed: 70
  average time/residue: 1.5511
  time to fit residues: 121.6343
Evaluate side-chains
  63 residues out of total 1231 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  194 ASP
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  413 ARG
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  767 TYR
Chi-restraints excluded: chain A residue  926 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 114 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 138 optimal weight:    2.9990
   chunk 149 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 110 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15427  Z= 0.199
  Angle     :  0.552   6.929  21619  Z= 0.296
  Chirality :  0.038   0.196   2510
  Planarity :  0.003   0.030   2136
  Dihedral  : 20.497 177.618   3900
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  8.61 %
    Favored  : 90.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.38 (0.23), residues: 1368
  helix:  0.89 (0.20), residues: 682
  sheet: -0.21 (0.41), residues: 155
  loop : -0.30 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1035 
 HIS   0.004   0.001   HIS A 206 
 PHE   0.016   0.001   PHE A 242 
 TYR   0.039   0.001   TYR A 767 
 ARG   0.003   0.000   ARG A 518 

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1231 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 1.645 
Fit side-chains
   revert: symmetry clash
REVERT: A  413 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8606 (ttp-170)
REVERT: A  440 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7613 (tm-30)
  outliers start: 15
  outliers final: 5
  residues processed: 74
  average time/residue: 1.4811
  time to fit residues: 122.5506
Evaluate side-chains
  58 residues out of total 1231 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  413 ARG
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1009 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 92 optimal weight:    2.9990
   chunk 138 optimal weight:    3.9990
   chunk 146 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  15427  Z= 0.360
  Angle     :  0.596   9.414  21619  Z= 0.317
  Chirality :  0.041   0.190   2510
  Planarity :  0.004   0.033   2136
  Dihedral  : 20.426 177.647   3900
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  9.67 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.51 (0.23), residues: 1368
  helix:  1.01 (0.20), residues: 682
  sheet: -0.19 (0.42), residues: 155
  loop : -0.24 (0.28), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1035 
 HIS   0.007   0.001   HIS A1105 
 PHE   0.022   0.001   PHE A 160 
 TYR   0.031   0.002   TYR A 767 
 ARG   0.004   0.000   ARG A1007 

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1231 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 1.681 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7279 (mmp)
REVERT: A  413 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8608 (ttp-170)
REVERT: A  440 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7578 (tm-30)
  outliers start: 17
  outliers final: 9
  residues processed: 66
  average time/residue: 1.6375
  time to fit residues: 120.5664
Evaluate side-chains
  57 residues out of total 1231 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  413 ARG
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  767 TYR
Chi-restraints excluded: chain A residue  988 VAL
Chi-restraints excluded: chain A residue 1009 LEU
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1381 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 109 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 125 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 131 optimal weight:    0.1980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: