Starting phenix.real_space_refine
on Tue Sep 24 14:45:19 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/09_2024/7nur_12600.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/09_2024/7nur_12600.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.125
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/09_2024/7nur_12600.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/09_2024/7nur_12600.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/09_2024/7nur_12600.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/09_2024/7nur_12600.cif"
  }
  resolution = 3.125
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    5307      2.51       5
     N    1417      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 8245
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1044, 8245
          Classifications: {'peptide': 1044}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 61, 'TRANS': 982}
          Chain breaks: 7
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
  Time building chain proxies: 5.52, per 1000 atoms: 0.67
  Number of scatterers: 8245
  At special positions: 0
  Unit cell: (89.712, 98.256, 120.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1490      8.00
     N    1417      7.00
     C    5307      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 688 " - pdb=" SG  CYS A 727 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1301 " - pdb=" SG  CYS A1359 " distance=2.03

  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: 2.04
  Conformation dependent library (CDL) restraints added in 935.1 milliseconds
  

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1980

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 5 sheets defined
      54.1% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 308 through 317
      removed outlier: 4.288A  pdb=" N   GLN A 312 " --> pdb=" O   PRO A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 383
      removed outlier: 3.610A  pdb=" N   GLY A 383 " --> pdb=" O   THR A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 404
      removed outlier: 4.007A  pdb=" N   ARG A 404 " --> pdb=" O   LYS A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 421
      removed outlier: 3.810A  pdb=" N   ARG A 418 " --> pdb=" O   ARG A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 436
      removed outlier: 4.000A  pdb=" N   ILE A 429 " --> pdb=" O   ASP A 425 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LYS A 430 " --> pdb=" O   VAL A 426 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   GLY A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 433 " --> pdb=" O   ILE A 429 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   ASP A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU A 436 " --> pdb=" O   MET A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 479
      removed outlier: 4.058A  pdb=" N   THR A 450 " --> pdb=" O   LYS A 446 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR A 464 " --> pdb=" O   GLU A 460 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ILE A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLN A 470 " --> pdb=" O   THR A 466 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ALA A 477 " --> pdb=" O   LYS A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 485
      removed outlier: 3.671A  pdb=" N   SER A 484 " --> pdb=" O   GLU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 505
      removed outlier: 3.969A  pdb=" N   TYR A 498 " --> pdb=" O   GLN A 494 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ALA A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 565
      removed outlier: 4.193A  pdb=" N   LEU A 561 " --> pdb=" O   GLY A 557 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLU A 563 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 578
      removed outlier: 3.697A  pdb=" N   LEU A 571 " --> pdb=" O   SER A 567 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER A 576 " --> pdb=" O   ILE A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 588
    Processing helix  chain 'A' and resid 597 through 599
      No H-bonds generated for 'chain 'A' and resid 597 through 599'
    Processing helix  chain 'A' and resid 638 through 642
    Processing helix  chain 'A' and resid 643 through 647
      removed outlier: 3.674A  pdb=" N   GLU A 647 " --> pdb=" O   PRO A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 673
      removed outlier: 3.969A  pdb=" N   TYR A 662 " --> pdb=" O   SER A 658 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ALA A 663 " --> pdb=" O   TYR A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 687
    Processing helix  chain 'A' and resid 689 through 694
    Processing helix  chain 'A' and resid 703 through 709
    Processing helix  chain 'A' and resid 718 through 729
      removed outlier: 3.884A  pdb=" N   TYR A 722 " --> pdb=" O   ALA A 718 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE A 728 " --> pdb=" O   LEU A 724 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA A 729 " --> pdb=" O   SER A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 737
    Processing helix  chain 'A' and resid 743 through 754
    Processing helix  chain 'A' and resid 763 through 783
    Processing helix  chain 'A' and resid 792 through 802
    Processing helix  chain 'A' and resid 804 through 813
    Processing helix  chain 'A' and resid 824 through 834
      removed outlier: 3.561A  pdb=" N   LEU A 831 " --> pdb=" O   SER A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 849
      removed outlier: 3.582A  pdb=" N   TYR A 845 " --> pdb=" O   LEU A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 860
      removed outlier: 3.521A  pdb=" N   PHE A 860 " --> pdb=" O   TYR A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 891
    Processing helix  chain 'A' and resid 896 through 908
    Processing helix  chain 'A' and resid 914 through 928
      removed outlier: 3.890A  pdb=" N   VAL A 918 " --> pdb=" O   GLY A 914 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   THR A 920 " --> pdb=" O   ARG A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 931 through 939
    Processing helix  chain 'A' and resid 941 through 950
      removed outlier: 3.562A  pdb=" N   TYR A 947 " --> pdb=" O   VAL A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 973
    Processing helix  chain 'A' and resid 982 through 1012
      removed outlier: 3.814A  pdb=" N   SER A 991 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA A 996 " --> pdb=" O   LYS A 992 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A1008 " --> pdb=" O   ALA A1004 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ARG A1009 " --> pdb=" O   ARG A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1028
      removed outlier: 3.738A  pdb=" N   GLY A1028 " --> pdb=" O   GLN A1024 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1032 through 1052
      removed outlier: 4.123A  pdb=" N   SER A1048 " --> pdb=" O   PHE A1044 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   VAL A1049 " --> pdb=" O   SER A1045 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1074
    Processing helix  chain 'A' and resid 1075 through 1082
      removed outlier: 3.879A  pdb=" N   LYS A1081 " --> pdb=" O   ALA A1077 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1086
    Processing helix  chain 'A' and resid 1092 through 1111
      removed outlier: 3.655A  pdb=" N   VAL A1106 " --> pdb=" O   ALA A1102 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR A1107 " --> pdb=" O   ALA A1103 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL A1108 " --> pdb=" O   VAL A1104 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   ARG A1109 " --> pdb=" O   ARG A1105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1129
    Processing helix  chain 'A' and resid 1129 through 1134
      removed outlier: 3.848A  pdb=" N   LYS A1133 " --> pdb=" O   ALA A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1146 through 1154
      removed outlier: 3.679A  pdb=" N   SER A1150 " --> pdb=" O   ARG A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1157 through 1185
      removed outlier: 3.576A  pdb=" N   GLU A1163 " --> pdb=" O   PRO A1159 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE A1167 " --> pdb=" O   GLU A1163 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TRP A1168 " --> pdb=" O   MET A1164 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR A1180 " --> pdb=" O   ILE A1176 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA A1181 " --> pdb=" O   ALA A1177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1240
      removed outlier: 4.290A  pdb=" N   ARG A1228 " --> pdb=" O   ALA A1224 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASP A1236 " --> pdb=" O   ARG A1232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1281 through 1294
      removed outlier: 3.621A  pdb=" N   GLN A1287 " --> pdb=" O   LEU A1283 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   PHE A1288 " --> pdb=" O   GLN A1284 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   PHE A1289 " --> pdb=" O   PHE A1285 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LYS A1294 " --> pdb=" O   THR A1290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1299 through 1303
      removed outlier: 3.772A  pdb=" N   ARG A1302 " --> pdb=" O   PRO A1299 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ARG A1303 " --> pdb=" O   GLN A1300 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1299 through 1303'
    Processing helix  chain 'A' and resid 1328 through 1332
    Processing helix  chain 'A' and resid 1363 through 1368
    Processing sheet with id=AA1, first strand: chain 'A' and resid 323 through 325
      removed outlier: 6.993A  pdb=" N   LEU A 324 " --> pdb=" O   LYS A 518 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   TRP A 526 " --> pdb=" O   PHE A 366 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE A 366 " --> pdb=" O   TRP A 526 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 528 " --> pdb=" O   LYS A 364 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLY A 334 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 592
    Processing sheet with id=AA3, first strand: chain 'A' and resid 601 through 604
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1246 through 1256
      removed outlier: 5.011A  pdb=" N   GLU A1268 " --> pdb=" O   GLY A1254 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1307 through 1309

    348 hydrogen bonds defined for protein.
    999 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.43

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2649
        1.34 -     1.46: 1638
        1.46 -     1.58: 4093
        1.58 -     1.70: 0
        1.70 -     1.81: 55
  Bond restraints: 8435
  Sorted by residual:
  bond pdb=" CA  GLU A 858 "
       pdb=" C   GLU A 858 "
    ideal  model  delta    sigma   weight residual
    1.523  1.481  0.043 1.80e-02 3.09e+03 5.59e+00
  bond pdb=" CA  ARG A 916 "
       pdb=" C   ARG A 916 "
    ideal  model  delta    sigma   weight residual
    1.522  1.489  0.032 1.72e-02 3.38e+03 3.55e+00
  bond pdb=" CB  THR A 881 "
       pdb=" CG2 THR A 881 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.10e+00
  bond pdb=" CB  VAL A 919 "
       pdb=" CG1 VAL A 919 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.77e+00
  bond pdb=" N   LYS A 940 "
       pdb=" CA  LYS A 940 "
    ideal  model  delta    sigma   weight residual
    1.456  1.472 -0.016 1.23e-02 6.61e+03 1.77e+00
  ... (remaining 8430 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 10984
        1.72 -     3.43: 371
        3.43 -     5.15: 52
        5.15 -     6.86: 11
        6.86 -     8.58: 5
  Bond angle restraints: 11423
  Sorted by residual:
  angle pdb=" CA  PHE A1062 "
        pdb=" C   PHE A1062 "
        pdb=" N   PRO A1063 "
      ideal   model   delta    sigma   weight residual
     117.82  120.83   -3.01 7.80e-01 1.64e+00 1.49e+01
  angle pdb=" CA  ALA A1206 "
        pdb=" C   ALA A1206 "
        pdb=" N   HIS A1207 "
      ideal   model   delta    sigma   weight residual
     118.43  123.29   -4.86 1.33e+00 5.65e-01 1.34e+01
  angle pdb=" C   THR A 953 "
        pdb=" N   GLN A 954 "
        pdb=" CA  GLN A 954 "
      ideal   model   delta    sigma   weight residual
     121.54  127.90   -6.36 1.91e+00 2.74e-01 1.11e+01
  angle pdb=" N   GLY A 621 "
        pdb=" CA  GLY A 621 "
        pdb=" C   GLY A 621 "
      ideal   model   delta    sigma   weight residual
     113.18  120.70   -7.52 2.37e+00 1.78e-01 1.01e+01
  angle pdb=" N   GLU A 958 "
        pdb=" CA  GLU A 958 "
        pdb=" C   GLU A 958 "
      ideal   model   delta    sigma   weight residual
     110.80  117.38   -6.58 2.13e+00 2.20e-01 9.55e+00
  ... (remaining 11418 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4598
       17.84 -    35.67: 414
       35.67 -    53.51: 85
       53.51 -    71.35: 7
       71.35 -    89.19: 7
  Dihedral angle restraints: 5111
    sinusoidal: 2066
      harmonic: 3045
  Sorted by residual:
  dihedral pdb=" CA  PRO A 817 "
           pdb=" C   PRO A 817 "
           pdb=" N   LEU A 818 "
           pdb=" CA  LEU A 818 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.40  -30.60     0      5.00e+00 4.00e-02 3.74e+01
  dihedral pdb=" CA  THR A 391 "
           pdb=" C   THR A 391 "
           pdb=" N   ASP A 392 "
           pdb=" CA  ASP A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.59  -30.41     0      5.00e+00 4.00e-02 3.70e+01
  dihedral pdb=" CA  CYS A1359 "
           pdb=" C   CYS A1359 "
           pdb=" N   PHE A1360 "
           pdb=" CA  PHE A1360 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.35   29.65     0      5.00e+00 4.00e-02 3.52e+01
  ... (remaining 5108 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 658
       0.031 -    0.062: 423
       0.062 -    0.094: 133
       0.094 -    0.125: 59
       0.125 -    0.156: 8
  Chirality restraints: 1281
  Sorted by residual:
  chirality pdb=" CA  VAL A 649 "
            pdb=" N   VAL A 649 "
            pdb=" C   VAL A 649 "
            pdb=" CB  VAL A 649 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CA  ILE A1274 "
            pdb=" N   ILE A1274 "
            pdb=" C   ILE A1274 "
            pdb=" CB  ILE A1274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.96e-01
  chirality pdb=" CA  ASP A 392 "
            pdb=" N   ASP A 392 "
            pdb=" C   ASP A 392 "
            pdb=" CB  ASP A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.16e-01
  ... (remaining 1278 not shown)

  Planarity restraints: 1456
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 855 "    0.037 5.00e-02 4.00e+02   5.66e-02 5.13e+00
        pdb=" N   PRO A 856 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 856 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 856 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 606 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO A 607 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 607 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 607 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1204 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO A1205 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A1205 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A1205 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1453 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 413
        2.72 -     3.26: 7972
        3.26 -     3.81: 11714
        3.81 -     4.35: 15023
        4.35 -     4.90: 26119
  Nonbonded interactions: 61241
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A1022 "
            pdb=" O   MET A1090 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OG  SER A1150 "
            pdb=" O   ALA A1156 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   SER A 975 "
            pdb=" OG  SER A 975 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ALA A 489 "
            pdb=" OG  SER A 490 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OD1 ASP A 519 "
            pdb=" N   LYS A 520 "
     model   vdw
     2.335 3.120
  ... (remaining 61236 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:             3.070
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     21.880
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
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   0.058   8435  Z= 0.434
  Angle     :  0.768   8.580  11423  Z= 0.435
  Chirality :  0.045   0.156   1281
  Planarity :  0.005   0.057   1456
  Dihedral  : 14.307  89.187   3125
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.68 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  9.81 %
    Favored  : 90.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.21), residues: 1028
  helix: -2.15 (0.19), residues: 520
  sheet: -2.95 (0.48), residues: 74
  loop : -3.34 (0.24), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 326 
 HIS   0.007   0.001   HIS A 804 
 PHE   0.016   0.002   PHE A 457 
 TYR   0.016   0.002   TYR A 774 
 ARG   0.008   0.001   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A  399 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.6013 (mt)
REVERT: A  846 GLN cc_start: 0.7513 (tp-100) cc_final: 0.7218 (mt0)
REVERT: A 1232 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.7068 (tpp-160)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.3230
  time to fit residues: 43.2586
Evaluate side-chains
  77 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 78 optimal weight:    0.4980
   chunk 43 optimal weight:    0.0970
   chunk 26 optimal weight:    0.4980
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0470
   chunk 60 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
A 558 ASN
A 766 HIS
A 801 GLN
** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 868 ASN
A 954 GLN
A 994 HIS
A1054 ASN
A1083 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8435  Z= 0.151
  Angle     :  0.556   6.904  11423  Z= 0.292
  Chirality :  0.040   0.143   1281
  Planarity :  0.005   0.051   1456
  Dihedral  :  5.303  33.289   1134
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.64 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 12.54 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.24), residues: 1028
  helix: -0.70 (0.22), residues: 522
  sheet: -2.18 (0.53), residues: 74
  loop : -2.71 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1218 
 HIS   0.005   0.001   HIS A 988 
 PHE   0.012   0.001   PHE A 808 
 TYR   0.012   0.001   TYR A 774 
 ARG   0.003   0.000   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 1.025 
Fit side-chains
REVERT: A 1237 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6380 (tm-30)
  outliers start: 7
  outliers final: 5
  residues processed: 95
  average time/residue: 0.2211
  time to fit residues: 28.5647
Evaluate side-chains
  81 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  382 GLN
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue 1055 TYR
Chi-restraints excluded: chain A residue 1308 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    0.0270
   chunk 29 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 102 optimal weight:   10.0000
   chunk 84 optimal weight:    0.0020
   chunk 93 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.4246

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8435  Z= 0.140
  Angle     :  0.508   6.394  11423  Z= 0.264
  Chirality :  0.039   0.142   1281
  Planarity :  0.005   0.052   1456
  Dihedral  :  4.800  28.385   1132
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.54 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.71 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.25), residues: 1028
  helix:  0.13 (0.23), residues: 521
  sheet: -1.64 (0.57), residues: 74
  loop : -2.41 (0.27), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1218 
 HIS   0.005   0.001   HIS A 593 
 PHE   0.011   0.001   PHE A 808 
 TYR   0.011   0.001   TYR A 458 
 ARG   0.003   0.000   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A 1237 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6396 (tm-30)
  outliers start: 9
  outliers final: 8
  residues processed: 85
  average time/residue: 0.2197
  time to fit residues: 25.5647
Evaluate side-chains
  80 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue 1055 TYR
Chi-restraints excluded: chain A residue 1075 MET
Chi-restraints excluded: chain A residue 1145 GLU
Chi-restraints excluded: chain A residue 1292 ILE
Chi-restraints excluded: chain A residue 1308 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 94 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1300 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8435  Z= 0.289
  Angle     :  0.582   7.367  11423  Z= 0.299
  Chirality :  0.042   0.135   1281
  Planarity :  0.005   0.051   1456
  Dihedral  :  5.059  28.211   1132
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.61 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 15.51 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.25), residues: 1028
  helix:  0.21 (0.23), residues: 522
  sheet: -1.41 (0.57), residues: 74
  loop : -2.33 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1218 
 HIS   0.006   0.001   HIS A 593 
 PHE   0.014   0.001   PHE A 808 
 TYR   0.015   0.002   TYR A 774 
 ARG   0.004   0.000   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A 1218 TRP cc_start: 0.8536 (m100) cc_final: 0.8212 (m-10)
  outliers start: 14
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1965
  time to fit residues: 24.3170
Evaluate side-chains
  87 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  632 ASP
Chi-restraints excluded: chain A residue  881 THR
Chi-restraints excluded: chain A residue 1055 TYR
Chi-restraints excluded: chain A residue 1145 GLU
Chi-restraints excluded: chain A residue 1246 VAL
Chi-restraints excluded: chain A residue 1292 ILE
Chi-restraints excluded: chain A residue 1308 VAL
Chi-restraints excluded: chain A residue 1325 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0030
   chunk 69 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 90 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.5590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8435  Z= 0.153
  Angle     :  0.501   6.621  11423  Z= 0.259
  Chirality :  0.039   0.143   1281
  Planarity :  0.005   0.049   1456
  Dihedral  :  4.707  27.645   1132
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.06 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.19 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.26), residues: 1028
  helix:  0.74 (0.23), residues: 516
  sheet: -1.11 (0.59), residues: 74
  loop : -2.16 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1218 
 HIS   0.004   0.001   HIS A 593 
 PHE   0.011   0.001   PHE A 808 
 TYR   0.011   0.001   TYR A 458 
 ARG   0.003   0.000   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A 1218 TRP cc_start: 0.8494 (m100) cc_final: 0.8236 (m-10)
REVERT: A 1232 ARG cc_start: 0.7498 (tpp-160) cc_final: 0.7270 (ttm-80)
REVERT: A 1237 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6376 (tm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 87
  average time/residue: 0.1911
  time to fit residues: 23.8144
Evaluate side-chains
  84 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue 1055 TYR
Chi-restraints excluded: chain A residue 1145 GLU
Chi-restraints excluded: chain A residue 1292 ILE
Chi-restraints excluded: chain A residue 1308 VAL
Chi-restraints excluded: chain A residue 1325 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8435  Z= 0.189
  Angle     :  0.516   6.776  11423  Z= 0.266
  Chirality :  0.040   0.139   1281
  Planarity :  0.005   0.049   1456
  Dihedral  :  4.711  27.248   1132
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.74 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.19 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.26), residues: 1028
  helix:  0.86 (0.23), residues: 516
  sheet: -0.98 (0.59), residues: 74
  loop : -2.12 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1218 
 HIS   0.005   0.001   HIS A 593 
 PHE   0.013   0.001   PHE A 808 
 TYR   0.012   0.001   TYR A 774 
 ARG   0.002   0.000   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  686 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7476 (mm-30)
REVERT: A 1218 TRP cc_start: 0.8495 (m100) cc_final: 0.8262 (m-10)
REVERT: A 1237 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6426 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 88
  average time/residue: 0.2167
  time to fit residues: 26.6569
Evaluate side-chains
  86 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  881 THR
Chi-restraints excluded: chain A residue 1055 TYR
Chi-restraints excluded: chain A residue 1145 GLU
Chi-restraints excluded: chain A residue 1246 VAL
Chi-restraints excluded: chain A residue 1292 ILE
Chi-restraints excluded: chain A residue 1308 VAL
Chi-restraints excluded: chain A residue 1325 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0470
   chunk 73 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7880

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8435  Z= 0.185
  Angle     :  0.517   6.799  11423  Z= 0.265
  Chirality :  0.039   0.138   1281
  Planarity :  0.005   0.050   1456
  Dihedral  :  4.677  26.856   1132
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.16 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.42 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.26), residues: 1028
  helix:  0.95 (0.23), residues: 518
  sheet: -0.85 (0.61), residues: 74
  loop : -2.01 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1218 
 HIS   0.004   0.001   HIS A 593 
 PHE   0.013   0.001   PHE A 808 
 TYR   0.012   0.001   TYR A 774 
 ARG   0.002   0.000   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A  622 ASP cc_start: 0.7606 (t0) cc_final: 0.7395 (t70)
REVERT: A 1237 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6396 (tm-30)
REVERT: A 1271 ARG cc_start: 0.8314 (ptp-110) cc_final: 0.8018 (mtp85)
  outliers start: 16
  outliers final: 12
  residues processed: 90
  average time/residue: 0.2135
  time to fit residues: 26.5600
Evaluate side-chains
  85 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  881 THR
Chi-restraints excluded: chain A residue 1055 TYR
Chi-restraints excluded: chain A residue 1145 GLU
Chi-restraints excluded: chain A residue 1246 VAL
Chi-restraints excluded: chain A residue 1292 ILE
Chi-restraints excluded: chain A residue 1308 VAL
Chi-restraints excluded: chain A residue 1325 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   chunk 91 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 93 optimal weight:    0.2980
   overall best weight:    1.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8435  Z= 0.245
  Angle     :  0.555   7.159  11423  Z= 0.284
  Chirality :  0.041   0.137   1281
  Planarity :  0.005   0.050   1456
  Dihedral  :  4.836  26.527   1132
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.32 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.65 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.26), residues: 1028
  helix:  0.79 (0.23), residues: 523
  sheet: -0.94 (0.59), residues: 72
  loop : -1.95 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1218 
 HIS   0.005   0.001   HIS A 593 
 PHE   0.014   0.001   PHE A 808 
 TYR   0.014   0.001   TYR A 774 
 ARG   0.003   0.000   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A  622 ASP cc_start: 0.7685 (t0) cc_final: 0.7466 (t70)
  outliers start: 14
  outliers final: 14
  residues processed: 83
  average time/residue: 0.1930
  time to fit residues: 22.9882
Evaluate side-chains
  84 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  632 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  881 THR
Chi-restraints excluded: chain A residue 1055 TYR
Chi-restraints excluded: chain A residue 1145 GLU
Chi-restraints excluded: chain A residue 1246 VAL
Chi-restraints excluded: chain A residue 1292 ILE
Chi-restraints excluded: chain A residue 1308 VAL
Chi-restraints excluded: chain A residue 1325 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1226 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8435  Z= 0.181
  Angle     :  0.521   6.896  11423  Z= 0.267
  Chirality :  0.039   0.138   1281
  Planarity :  0.005   0.050   1456
  Dihedral  :  4.696  26.831   1132
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.06 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.88 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.26), residues: 1028
  helix:  0.99 (0.23), residues: 520
  sheet: -0.88 (0.60), residues: 72
  loop : -1.93 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 997 
 HIS   0.005   0.001   HIS A 593 
 PHE   0.013   0.001   PHE A 808 
 TYR   0.012   0.001   TYR A 774 
 ARG   0.002   0.000   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A 1237 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6515 (tm-30)
REVERT: A 1271 ARG cc_start: 0.8339 (ptp-110) cc_final: 0.8024 (mtp85)
  outliers start: 16
  outliers final: 14
  residues processed: 86
  average time/residue: 0.2045
  time to fit residues: 24.6204
Evaluate side-chains
  85 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  632 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  881 THR
Chi-restraints excluded: chain A residue 1055 TYR
Chi-restraints excluded: chain A residue 1145 GLU
Chi-restraints excluded: chain A residue 1246 VAL
Chi-restraints excluded: chain A residue 1292 ILE
Chi-restraints excluded: chain A residue 1308 VAL
Chi-restraints excluded: chain A residue 1325 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 82 optimal weight:    0.4980
   chunk 8 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8435  Z= 0.169
  Angle     :  0.508   6.716  11423  Z= 0.261
  Chirality :  0.039   0.139   1281
  Planarity :  0.005   0.050   1456
  Dihedral  :  4.607  26.558   1132
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.35 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.88 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.26), residues: 1028
  helix:  1.12 (0.23), residues: 519
  sheet: -0.79 (0.60), residues: 72
  loop : -1.89 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 997 
 HIS   0.004   0.001   HIS A 593 
 PHE   0.012   0.001   PHE A 808 
 TYR   0.011   0.001   TYR A 774 
 ARG   0.002   0.000   ARG A 648 

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A 1237 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6611 (tm-30)
REVERT: A 1271 ARG cc_start: 0.8257 (ptp-110) cc_final: 0.8021 (mtp85)
  outliers start: 15
  outliers final: 15
  residues processed: 86
  average time/residue: 0.2165
  time to fit residues: 26.1121
Evaluate side-chains
  85 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  632 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  881 THR
Chi-restraints excluded: chain A residue 1055 TYR
Chi-restraints excluded: chain A residue 1145 GLU
Chi-restraints excluded: chain A residue 1246 VAL
Chi-restraints excluded: chain A residue 1292 ILE
Chi-restraints excluded: chain A residue 1308 VAL
Chi-restraints excluded: chain A residue 1325 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 82 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 525 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.138831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.107915 restraints weight = 10235.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.39
r_work: 0.3015 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8435  Z= 0.224
  Angle     :  0.539   7.014  11423  Z= 0.276
  Chirality :  0.040   0.135   1281
  Planarity :  0.005   0.050   1456
  Dihedral  :  4.712  26.260   1132
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.23 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.76 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.26), residues: 1028
  helix:  0.94 (0.23), residues: 526
  sheet: -0.79 (0.60), residues: 72
  loop : -1.85 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 997 
 HIS   0.005   0.001   HIS A 593 
 PHE   0.014   0.001   PHE A 808 
 TYR   0.013   0.001   TYR A 774 
 ARG   0.002   0.000   ARG A 648 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1978.30 seconds
wall clock time: 35 minutes 42.53 seconds (2142.53 seconds total)