Starting phenix.real_space_refine
on Thu Feb 15 03:09:29 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xso_33429/02_2024/7xso_33429.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xso_33429/02_2024/7xso_33429.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xso_33429/02_2024/7xso_33429.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xso_33429/02_2024/7xso_33429.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xso_33429/02_2024/7xso_33429.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xso_33429/02_2024/7xso_33429.pdb"
  }
  resolution = 3.01
  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=   0.004 sd=   0.047
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
     Zn      4      6.06       5
     P      35      5.49       5
     S      33      5.16       5
     C    6836      2.51       5
     N    1913      2.21       5
     O    2150      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   11": "OE1" <-> "OE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   22": "OE1" <-> "OE2"
    Residue "A GLU   72": "OE1" <-> "OE2"
    Residue "A GLU   73": "OE1" <-> "OE2"
    Residue "A GLU   83": "OE1" <-> "OE2"
    Residue "A GLU  124": "OE1" <-> "OE2"
    Residue "A GLU  144": "OE1" <-> "OE2"
    Residue "A TYR  149": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  200": "OE1" <-> "OE2"
    Residue "A GLU  214": "OE1" <-> "OE2"
    Residue "A GLU  267": "OE1" <-> "OE2"
    Residue "A GLU  278": "OE1" <-> "OE2"
    Residue "A GLU  282": "OE1" <-> "OE2"
    Residue "A GLU  308": "OE1" <-> "OE2"
    Residue "A GLU  360": "OE1" <-> "OE2"
    Residue "A TYR  390": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  397": "OE1" <-> "OE2"
    Residue "A PHE  428": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  443": "OE1" <-> "OE2"
    Residue "A GLU  454": "OE1" <-> "OE2"
    Residue "A GLU  465": "OE1" <-> "OE2"
    Residue "A GLU  549": "OE1" <-> "OE2"
    Residue "A GLU  581": "OE1" <-> "OE2"
    Residue "A GLU  620": "OE1" <-> "OE2"
    Residue "A GLU  624": "OE1" <-> "OE2"
    Residue "A GLU  633": "OE1" <-> "OE2"
    Residue "A GLU  639": "OE1" <-> "OE2"
    Residue "A GLU  653": "OE1" <-> "OE2"
    Residue "A GLU  654": "OE1" <-> "OE2"
    Residue "A GLU  656": "OE1" <-> "OE2"
    Residue "A GLU  677": "OE1" <-> "OE2"
    Residue "A GLU  693": "OE1" <-> "OE2"
    Residue "A GLU  745": "OE1" <-> "OE2"
    Residue "A GLU  748": "OE1" <-> "OE2"
    Residue "A GLU  761": "OE1" <-> "OE2"
    Residue "A GLU  784": "OE1" <-> "OE2"
    Residue "A PHE  824": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  878": "OE1" <-> "OE2"
    Residue "A GLU  936": "OE1" <-> "OE2"
    Residue "A ASP  938": "OD1" <-> "OD2"
    Residue "A GLU  944": "OE1" <-> "OE2"
    Residue "A GLU  972": "OE1" <-> "OE2"
    Residue "A GLU 1002": "OE1" <-> "OE2"
    Residue "A PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1437": "OE1" <-> "OE2"
    Residue "A GLU 1441": "OE1" <-> "OE2"
    Residue "A GLU 1472": "OE1" <-> "OE2"
    Residue "A GLU 1496": "OE1" <-> "OE2"
    Residue "A GLU 1589": "OE1" <-> "OE2"
    Residue "A GLU 1640": "OE1" <-> "OE2"
    Residue "A PHE 1691": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 10971
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 10232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1271, 10232
          Classifications: {'peptide': 1271}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 60, 'TRANS': 1210}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 735
          Classifications: {'RNA': 35}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 18, 'rna3p': 16}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    676  SG  CYS A  88      77.755  24.345  20.422  1.00 56.77           S
  ATOM    947  SG  CYS A 121      81.150  23.663  18.457  1.00 61.88           S
  ATOM    993  SG  CYS A 127      80.468  27.509  19.938  1.00 55.76           S
  ATOM   1017  SG  CYS A 130      81.117  24.681  22.142  1.00 54.16           S
  ATOM   3605  SG  CYS A 491      55.617  30.294  46.468  1.00 54.94           S
  ATOM   3673  SG  CYS A 501      56.577  28.803  43.330  1.00 54.99           S
  ATOM   3687  SG  CYS A 503      54.317  32.071  42.736  1.00 54.55           S
  ATOM   3709  SG  CYS A 506      57.891  32.628  43.859  1.00 50.92           S
  ATOM   5680  SG  CYS A 750      41.443  35.171  73.361  1.00 67.60           S
  ATOM   5693  SG  CYS A 752      39.561  38.582  72.519  1.00 60.45           S
  ATOM   5715  SG  CYS A 755      43.237  38.815  71.688  1.00 54.67           S
  ATOM   7689  SG  CYS A1018      41.329  59.400 103.367  1.00 44.86           S
  ATOM   7914  SG  CYS A1406      42.342  55.852 102.186  1.00 50.92           S
  ATOM   7965  SG  CYS A1414      38.269  57.860 101.887  1.00 45.70           S
  ATOM   7982  SG  CYS A1417      41.074  58.599  99.691  1.00 42.97           S

  Time building chain proxies: 6.12, per 1000 atoms: 0.56
  Number of scatterers: 10971
  At special positions: 0
  Unit cell: (111.15, 115.425, 140.22, 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)
     Zn      4     29.99
     S      33     16.00
     P      35     15.00
     O    2150      8.00
     N    1913      7.00
     C    6836      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 9.09
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1801 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 127 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A  88 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 130 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 121 "
      pdb="  ZN A1802 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 491 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 506 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 503 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 501 "
      pdb="  ZN A1803 "
        pdb="ZN    ZN A1803 " - pdb=" ND1 HIS A 747 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 752 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 750 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 755 "
      pdb="  ZN A1804 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1406 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1018 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1414 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1417 "
      Number of angles added : 21


  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2324

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 17 sheets defined
      29.0% alpha, 22.5% beta
      0 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 3.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 31
      removed outlier: 3.570A  pdb=" N   LYS A  30 " --> pdb=" O   TRP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 38
    Processing helix  chain 'A' and resid 59 through 78
      removed outlier: 3.605A  pdb=" N   VAL A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 134
    Processing helix  chain 'A' and resid 169 through 172
      No H-bonds generated for 'chain 'A' and resid 169 through 172'
    Processing helix  chain 'A' and resid 214 through 224
      removed outlier: 4.166A  pdb=" N   LEU A 219 " --> pdb=" O   HIS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 287
      removed outlier: 3.848A  pdb=" N   ASN A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 303
      removed outlier: 4.226A  pdb=" N   ILE A 295 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 307
      removed outlier: 5.788A  pdb=" N   GLY A 307 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 304 through 307'
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 338 through 348
    Processing helix  chain 'A' and resid 354 through 375
      removed outlier: 3.554A  pdb=" N   PHE A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 488
    Processing helix  chain 'A' and resid 503 through 510
    Processing helix  chain 'A' and resid 569 through 580
      removed outlier: 3.526A  pdb=" N   SER A 573 " --> pdb=" O   PRO A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 598
    Processing helix  chain 'A' and resid 617 through 625
    Processing helix  chain 'A' and resid 626 through 628
      No H-bonds generated for 'chain 'A' and resid 626 through 628'
    Processing helix  chain 'A' and resid 631 through 637
      removed outlier: 3.952A  pdb=" N   LEU A 635 " --> pdb=" O   GLU A 631 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   GLU A 636 " --> pdb=" O   LYS A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 658
      removed outlier: 3.530A  pdb=" N   CYS A 657 " --> pdb=" O   GLU A 654 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 658 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 654 through 658'
    Processing helix  chain 'A' and resid 665 through 667
      No H-bonds generated for 'chain 'A' and resid 665 through 667'
    Processing helix  chain 'A' and resid 688 through 692
    Processing helix  chain 'A' and resid 723 through 739
      removed outlier: 3.627A  pdb=" N   HIS A 727 " --> pdb=" O   LYS A 723 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ARG A 738 " --> pdb=" O   ALA A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 758
    Processing helix  chain 'A' and resid 831 through 848
    Processing helix  chain 'A' and resid 855 through 859
    Processing helix  chain 'A' and resid 873 through 881
      removed outlier: 3.523A  pdb=" N   LYS A 877 " --> pdb=" O   PRO A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 914
      removed outlier: 3.813A  pdb=" N   ASP A 914 " --> pdb=" O   SER A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1015
      removed outlier: 3.848A  pdb=" N   LEU A1003 " --> pdb=" O   PRO A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1414 through 1421
    Processing helix  chain 'A' and resid 1486 through 1493
      removed outlier: 3.816A  pdb=" N   ILE A1490 " --> pdb=" O   GLY A1486 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LYS A1493 " --> pdb=" O   ILE A1489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1493 through 1499
    Processing helix  chain 'A' and resid 1528 through 1540
      removed outlier: 3.540A  pdb=" N   ASP A1540 " --> pdb=" O   LEU A1536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1583 through 1603
    Processing helix  chain 'A' and resid 1615 through 1618
      removed outlier: 3.600A  pdb=" N   VAL A1618 " --> pdb=" O   GLN A1615 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1615 through 1618'
    Processing helix  chain 'A' and resid 1619 through 1629
    Processing helix  chain 'A' and resid 1673 through 1683
    Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153
      removed outlier: 3.699A  pdb=" N   LEU A 158 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   SER A  56 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   ALA A  53 " --> pdb=" O   LYS A  47 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TRP A 195 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      removed outlier: 9.409A  pdb=" N   GLU A  22 " --> pdb=" O   ARG A 193 " (cutoff:3.500A)
      removed outlier: 13.588A  pdb=" N   ARG A 193 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP A 190 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE A 192 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168
      removed outlier: 3.966A  pdb=" N   LEU A 167 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   SER A  56 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 158 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   THR A   9 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82
    Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111
      removed outlier: 6.184A  pdb=" N   THR A 110 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 514
      removed outlier: 6.616A  pdb=" N   GLU A 415 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   GLU A 611 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE A 417 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   ILE A 609 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A 419 " --> pdb=" O   ILE A 607 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ILE A 607 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   GLY A 600 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514
      removed outlier: 6.616A  pdb=" N   GLU A 415 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   GLU A 611 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE A 417 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   ILE A 609 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A 419 " --> pdb=" O   ILE A 607 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ILE A 607 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432
      removed outlier: 3.788A  pdb=" N   VAL A 432 " --> pdb=" O   ASN A 459 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ASN A 459 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 470
    Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 530
    Processing sheet with id=AB1, first strand: chain 'A' and resid 533 through 534
      removed outlier: 3.804A  pdb=" N   THR A 539 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704
      removed outlier: 3.777A  pdb=" N   ARG A 719 " --> pdb=" O   LYS A 704 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   PHE A 720 " --> pdb=" O   LEU A 774 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704
      removed outlier: 3.777A  pdb=" N   ARG A 719 " --> pdb=" O   LYS A 704 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   PHE A 720 " --> pdb=" O   LEU A 774 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 789
    Processing sheet with id=AB5, first strand: chain 'A' and resid 924 through 927
    Processing sheet with id=AB6, first strand: chain 'A' and resid 991 through 992
      removed outlier: 6.562A  pdb=" N   LEU A 996 " --> pdb=" O   TYR A1436 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   VAL A1517 " --> pdb=" O   GLU A1437 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992
      removed outlier: 6.562A  pdb=" N   LEU A 996 " --> pdb=" O   TYR A1436 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   VAL A1517 " --> pdb=" O   GLU A1437 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   VAL A1517 " --> pdb=" O   THR A 960 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   THR A 960 " --> pdb=" O   VAL A1517 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   SER A1519 " --> pdb=" O   LEU A 958 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   LEU A 958 " --> pdb=" O   SER A1519 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   ASP A1521 " --> pdb=" O   CYS A 956 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   CYS A 956 " --> pdb=" O   ASP A1521 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   ARG A1523 " --> pdb=" O   ILE A 954 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   ILE A 954 " --> pdb=" O   ARG A1523 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   GLU A1525 " --> pdb=" O   GLY A 952 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   GLY A 952 " --> pdb=" O   GLU A1525 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LYS A 957 " --> pdb=" O   ILE A1564 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   ILE A1564 " --> pdb=" O   LYS A 957 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   GLU A 959 " --> pdb=" O   ILE A1562 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   ILE A1562 " --> pdb=" O   GLU A 959 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 985 through 987
      removed outlier: 6.555A  pdb=" N   LYS A 985 " --> pdb=" O   THR A1508 " (cutoff:3.500A)

    358 hydrogen bonds defined for protein.
    987 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 4.93

  Time building geometry restraints manager: 4.29 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1766
        1.28 -     1.41: 2987
        1.41 -     1.54: 6409
        1.54 -     1.68: 85
        1.68 -     1.81: 45
  Bond restraints: 11292
  Sorted by residual:
  bond pdb=" C   PRO A1687 "
       pdb=" O   PRO A1687 "
    ideal  model  delta    sigma   weight residual
    1.233  1.149  0.084 1.16e-02 7.43e+03 5.20e+01
  bond pdb=" O3'   C D  15 "
       pdb=" P     G D  16 "
    ideal  model  delta    sigma   weight residual
    1.607  1.500  0.107 1.50e-02 4.44e+03 5.13e+01
  bond pdb=" C   PRO A1690 "
       pdb=" O   PRO A1690 "
    ideal  model  delta    sigma   weight residual
    1.235  1.183  0.052 7.90e-03 1.60e+04 4.40e+01
  bond pdb=" O3'   U D  -2 "
       pdb=" P     A D  -1 "
    ideal  model  delta    sigma   weight residual
    1.607  1.517  0.090 1.50e-02 4.44e+03 3.63e+01
  bond pdb=" C   PRO A1684 "
       pdb=" O   PRO A1684 "
    ideal  model  delta    sigma   weight residual
    1.234  1.169  0.065 1.14e-02 7.69e+03 3.22e+01
  ... (remaining 11287 not shown)

  Histogram of bond angle deviations from ideal:
       93.66 -   101.82: 68
      101.82 -   109.97: 2319
      109.97 -   118.13: 6308
      118.13 -   126.28: 6411
      126.28 -   134.44: 285
  Bond angle restraints: 15391
  Sorted by residual:
  angle pdb=" N   PRO A1690 "
        pdb=" CA  PRO A1690 "
        pdb=" C   PRO A1690 "
      ideal   model   delta    sigma   weight residual
     110.74   93.66   17.08 1.66e+00 3.63e-01 1.06e+02
  angle pdb=" N   LEU A 975 "
        pdb=" CA  LEU A 975 "
        pdb=" C   LEU A 975 "
      ideal   model   delta    sigma   weight residual
     113.30  103.67    9.63 1.34e+00 5.57e-01 5.17e+01
  angle pdb=" O3'   C D  -7 "
        pdb=" C3'   C D  -7 "
        pdb=" C2'   C D  -7 "
      ideal   model   delta    sigma   weight residual
     113.70  104.35    9.35 1.50e+00 4.44e-01 3.89e+01
  angle pdb=" O2'   C D  -7 "
        pdb=" C2'   C D  -7 "
        pdb=" C1'   C D  -7 "
      ideal   model   delta    sigma   weight residual
     108.40   99.06    9.34 1.50e+00 4.44e-01 3.87e+01
  angle pdb=" O4'   A D  -1 "
        pdb=" C1'   A D  -1 "
        pdb=" C2'   A D  -1 "
      ideal   model   delta    sigma   weight residual
     105.80  100.12    5.68 1.00e+00 1.00e+00 3.22e+01
  ... (remaining 15386 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.24: 6534
       35.24 -    70.47: 261
       70.47 -   105.71: 19
      105.71 -   140.95: 0
      140.95 -   176.18: 9
  Dihedral angle restraints: 6823
    sinusoidal: 3192
      harmonic: 3631
  Sorted by residual:
  dihedral pdb=" O4'   U D -13 "
           pdb=" C1'   U D -13 "
           pdb=" N1    U D -13 "
           pdb=" C2    U D -13 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   16.18 -176.18     1      1.50e+01 4.44e-03 8.52e+01
  dihedral pdb=" O4'   U D -10 "
           pdb=" C1'   U D -10 "
           pdb=" N1    U D -10 "
           pdb=" C2    U D -10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   32.16  167.84     1      1.50e+01 4.44e-03 8.44e+01
  dihedral pdb=" O4'   U D   8 "
           pdb=" C1'   U D   8 "
           pdb=" N1    U D   8 "
           pdb=" C2    U D   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   41.91  158.09     1      1.50e+01 4.44e-03 8.23e+01
  ... (remaining 6820 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1441
       0.092 -    0.185: 182
       0.185 -    0.277: 24
       0.277 -    0.369: 5
       0.369 -    0.461: 1
  Chirality restraints: 1653
  Sorted by residual:
  chirality pdb=" CA  ASN A1649 "
            pdb=" N   ASN A1649 "
            pdb=" C   ASN A1649 "
            pdb=" CB  ASN A1649 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.32e+00
  chirality pdb=" C1'   U D -13 "
            pdb=" O4'   U D -13 "
            pdb=" C2'   U D -13 "
            pdb=" N1    U D -13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.10    0.37 2.00e-01 2.50e+01 3.37e+00
  chirality pdb=" CA  PRO A1690 "
            pdb=" N   PRO A1690 "
            pdb=" C   PRO A1690 "
            pdb=" CB  PRO A1690 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    3.05   -0.33 2.00e-01 2.50e+01 2.73e+00
  ... (remaining 1650 not shown)

  Planarity restraints: 1868
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 391 "   -0.018 2.00e-02 2.50e+03   3.73e-02 1.39e+01
        pdb=" C   SER A 391 "    0.064 2.00e-02 2.50e+03
        pdb=" O   SER A 391 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LYS A 392 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  -1 "    0.047 2.00e-02 2.50e+03   2.19e-02 1.31e+01
        pdb=" N9    A D  -1 "   -0.050 2.00e-02 2.50e+03
        pdb=" C8    A D  -1 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  -1 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A D  -1 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A D  -1 "    0.010 2.00e-02 2.50e+03
        pdb=" N6    A D  -1 "    0.003 2.00e-02 2.50e+03
        pdb=" N1    A D  -1 "    0.014 2.00e-02 2.50e+03
        pdb=" C2    A D  -1 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3    A D  -1 "   -0.013 2.00e-02 2.50e+03
        pdb=" C4    A D  -1 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 972 "    0.016 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   GLU A 972 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   GLU A 972 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ASN A 973 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1865 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 501
        2.71 -     3.25: 9439
        3.25 -     3.80: 16900
        3.80 -     4.35: 21160
        4.35 -     4.90: 36860
  Nonbonded interactions: 84860
  Sorted by model distance:
  nonbonded pdb=" O   SER A 438 "
            pdb=" OG  SER A 438 "
     model   vdw
     2.157 2.440
  nonbonded pdb=" O   THR A 751 "
            pdb=" OG1 THR A 751 "
     model   vdw
     2.316 2.440
  nonbonded pdb=" OH  TYR A1645 "
            pdb=" OP1   C D  14 "
     model   vdw
     2.327 2.440
  nonbonded pdb=" OG  SER A 813 "
            pdb=" OE1 GLU A 995 "
     model   vdw
     2.330 2.440
  nonbonded pdb=" OD1 ASN A1448 "
            pdb=" NH1 ARG A1498 "
     model   vdw
     2.338 2.520
  ... (remaining 84855 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:             0.580
  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:          3.480
  Check model and map are aligned:         0.170
  Set scattering table:                    0.120
  Process input model:                     36.350
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
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      :  0.009   0.107  11292  Z= 0.598
  Angle     :  1.020  17.076  15391  Z= 0.614
  Chirality :  0.066   0.461   1653
  Planarity :  0.008   0.082   1868
  Dihedral  : 18.965 176.183   4499
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.96 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 14.60 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.34 %
  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: -2.97 (0.19), residues: 1259
  helix: -2.12 (0.21), residues: 321
  sheet: -0.33 (0.34), residues: 208
  loop : -2.49 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A1685 
 HIS   0.009   0.002   HIS A 924 
 PHE   0.023   0.003   PHE A 192 
 TYR   0.019   0.002   TYR A 860 
 ARG   0.008   0.001   ARG A 323 

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1111 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 264
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.5940 (m-30)
REVERT: A   51 ARG cc_start: 0.8520 (ptp-170) cc_final: 0.8279 (mtp-110)
REVERT: A   73 GLU cc_start: 0.7227 (tt0) cc_final: 0.6854 (mt-10)
REVERT: A  142 VAL cc_start: 0.8871 (t) cc_final: 0.8487 (p)
REVERT: A  287 ASN cc_start: 0.8153 (m110) cc_final: 0.7895 (m110)
REVERT: A  291 GLU cc_start: 0.7169 (tp30) cc_final: 0.6959 (tp30)
REVERT: A  293 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7573 (tp)
REVERT: A  318 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6242 (p0)
REVERT: A  334 VAL cc_start: 0.8029 (t) cc_final: 0.7756 (m)
REVERT: A  401 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8137 (tp)
REVERT: A  509 MET cc_start: 0.8247 (mmm) cc_final: 0.7419 (mmm)
REVERT: A  567 LYS cc_start: 0.8244 (ptmt) cc_final: 0.8023 (ptmm)
REVERT: A  581 GLU cc_start: 0.6926 (pp20) cc_final: 0.6581 (pp20)
REVERT: A  623 LYS cc_start: 0.8259 (ttmt) cc_final: 0.8022 (ttpp)
REVERT: A  646 LEU cc_start: 0.7862 (tp) cc_final: 0.7661 (tp)
REVERT: A  651 PHE cc_start: 0.8274 (m-80) cc_final: 0.7820 (m-80)
REVERT: A  653 GLU cc_start: 0.6614 (mp0) cc_final: 0.6309 (mp0)
REVERT: A  689 SER cc_start: 0.8436 (m) cc_final: 0.8037 (t)
REVERT: A  778 ASN cc_start: 0.8190 (p0) cc_final: 0.7956 (p0)
REVERT: A  847 ASP cc_start: 0.7148 (m-30) cc_final: 0.6917 (m-30)
REVERT: A  944 GLU cc_start: 0.7397 (pm20) cc_final: 0.7042 (pm20)
REVERT: A 1488 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7398 (mtt180)
REVERT: A 1489 ILE cc_start: 0.8124 (pt) cc_final: 0.7875 (mp)
REVERT: A 1493 LYS cc_start: 0.8230 (ptpp) cc_final: 0.7988 (pttp)
REVERT: A 1497 ILE cc_start: 0.8047 (mm) cc_final: 0.7815 (mt)
REVERT: A 1570 PHE cc_start: 0.7920 (p90) cc_final: 0.7340 (p90)
  outliers start: 44
  outliers final: 18
  residues processed: 299
  average time/residue: 0.2222
  time to fit residues: 87.8391
Evaluate side-chains
  238 residues out of total 1111 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 216
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  980 ASN
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1637 SER
Chi-restraints excluded: chain A residue 1653 LYS
Chi-restraints excluded: chain A residue 1656 ILE
Chi-restraints excluded: chain A residue 1679 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 118 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 492 ASN
A 708 ASN
A 871 ASN
A 901 ASN
A1544 ASN
A1604 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11292  Z= 0.174
  Angle     :  0.566   7.358  15391  Z= 0.296
  Chirality :  0.043   0.250   1653
  Planarity :  0.006   0.065   1868
  Dihedral  : 18.342 176.944   1963
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.22 %
    Favored  : 76.34 %
  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: -1.64 (0.21), residues: 1259
  helix: -0.11 (0.28), residues: 329
  sheet: -0.05 (0.35), residues: 199
  loop : -1.95 (0.19), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 612 
 HIS   0.004   0.001   HIS A 727 
 PHE   0.017   0.001   PHE A 546 
 TYR   0.015   0.001   TYR A 808 
 ARG   0.002   0.000   ARG A 304 

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1111 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 216
  time to evaluate  : 1.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.5863 (m-30)
REVERT: A  287 ASN cc_start: 0.8003 (m110) cc_final: 0.7753 (m110)
REVERT: A  509 MET cc_start: 0.8306 (mmm) cc_final: 0.7245 (mmm)
REVERT: A  567 LYS cc_start: 0.8276 (ptmt) cc_final: 0.8037 (ptmm)
REVERT: A  623 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7977 (ttpp)
REVERT: A  651 PHE cc_start: 0.8257 (m-80) cc_final: 0.7818 (m-80)
REVERT: A  653 GLU cc_start: 0.6758 (mp0) cc_final: 0.6439 (mp0)
REVERT: A  689 SER cc_start: 0.8150 (m) cc_final: 0.7936 (p)
REVERT: A  719 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7618 (mtt90)
REVERT: A  821 LYS cc_start: 0.8082 (tttt) cc_final: 0.7800 (tttp)
REVERT: A  944 GLU cc_start: 0.7341 (pm20) cc_final: 0.6956 (pm20)
REVERT: A  977 LEU cc_start: 0.8139 (mt) cc_final: 0.7930 (mp)
REVERT: A 1497 ILE cc_start: 0.7995 (mm) cc_final: 0.7750 (mt)
REVERT: A 1570 PHE cc_start: 0.8020 (p90) cc_final: 0.7520 (p90)
  outliers start: 38
  outliers final: 21
  residues processed: 240
  average time/residue: 0.2114
  time to fit residues: 67.6679
Evaluate side-chains
  235 residues out of total 1111 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 213
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  751 THR
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  980 ASN
Chi-restraints excluded: chain A residue 1411 ASP
Chi-restraints excluded: chain A residue 1582 VAL
Chi-restraints excluded: chain A residue 1637 SER
Chi-restraints excluded: chain A residue 1653 LYS
Chi-restraints excluded: chain A residue 1656 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 118 optimal weight:    1.9990
   chunk 127 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 40 optimal weight:    0.3980
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 498 GLN
A 901 ASN
A 993 ASN
A1537 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2380
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_fail.pdb'.
Return code: -15
Dumping stderr: