Starting phenix.real_space_refine
on Wed Nov 15 23:21:59 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2023/7m1p_23617.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2023/7m1p_23617.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2023/7m1p_23617.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2023/7m1p_23617.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2023/7m1p_23617.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2023/7m1p_23617.pdb"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.984
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      51      5.16       5
     C    8662      2.51       5
     N    2322      2.21       5
     O    2476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP  613": "OD1" <-> "OD2"
    Residue "A GLU  616": "OE1" <-> "OE2"
    Residue "A PHE  961": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1889": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 13511
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 13340
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1938, 13331
          Classifications: {'peptide': 1938}
          Incomplete info: {'truncation_to_alanine': 579}
          Link IDs: {'PTRANS': 100, 'TRANS': 1837}
          Chain breaks: 13
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 2175
          Unresolved non-hydrogen angles: 2757
          Unresolved non-hydrogen dihedrals: 1789
          Unresolved non-hydrogen chiralities: 188
          Planarities with less than four sites: {'GLN:plan1': 27, 'ASP:plan': 53, 'TYR:plan': 14, 'ASN:plan1': 25, 'TRP:plan': 10, 'HIS:plan': 14, 'PHE:plan': 27, 'GLU:plan': 71, 'ARG:plan': 42}
          Unresolved non-hydrogen planarities: 1246
      Conformer: "B"
        Number of residues, atoms: 1938, 13331
          Classifications: {'peptide': 1938}
          Incomplete info: {'truncation_to_alanine': 579}
          Link IDs: {'PTRANS': 100, 'TRANS': 1837}
          Chain breaks: 13
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 2175
          Unresolved non-hydrogen angles: 2757
          Unresolved non-hydrogen dihedrals: 1789
          Unresolved non-hydrogen chiralities: 188
          Planarities with less than four sites: {'GLN:plan1': 27, 'ASP:plan': 53, 'TYR:plan': 14, 'ASN:plan1': 25, 'TRP:plan': 10, 'HIS:plan': 14, 'PHE:plan': 27, 'GLU:plan': 71, 'ARG:plan': 42}
          Unresolved non-hydrogen planarities: 1246
          bond proxies already assigned to first conformer: 13615
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen chiralities: 5
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 13.81, per 1000 atoms: 1.02
  Number of scatterers: 13511
  At special positions: 0
  Unit cell: (96.7808, 93.6921, 229.597, 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      51     16.00
     O    2476      8.00
     N    2322      7.00
     C    8662      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 324 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 519 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 641 " - pdb=" SG  CYS A1490 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1488 " - pdb=" SG  CYS A1502 " distance=2.03

  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
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A2301 " - " ASN A  98 "
      " NAG A2302 " - " ASN A 504 "
      " NAG A2303 " - " ASN A1588 "
      " NAG B   1 " - " ASN A 415 "
      " NAG C   1 " - " ASN A1529 "
      " NAG D   1 " - " ASN A1662 "
  Time building additional restraints: 5.85
  Conformation dependent library (CDL) restraints added in 5.7 seconds
  

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3642

  Finding SS restraints...
    Secondary structure from input PDB file:
      83 helices and 10 sheets defined
      51.5% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 22
      removed outlier: 3.871A  pdb=" N   LEU A   9 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LYS A  22 " --> pdb=" O   ARG A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 46
      removed outlier: 3.539A  pdb=" N   VAL A  27 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      Proline residue:  A  32  - end of helix
      removed outlier: 3.531A  pdb=" N   VAL A  38 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 65 through 76
      removed outlier: 3.711A  pdb=" N   TRP A  69 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 90
    Processing helix  chain 'A' and resid 100 through 109
    Processing helix  chain 'A' and resid 118 through 129
      removed outlier: 4.226A  pdb=" N   LEU A 122 " --> pdb=" O   GLU A 118 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG A 124 " --> pdb=" O   GLN A 120 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LEU A 129 " --> pdb=" O   ILE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 289
    Processing helix  chain 'A' and resid 292 through 297
      removed outlier: 3.751A  pdb=" N   LEU A 296 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 305
      removed outlier: 4.179A  pdb=" N   LEU A 303 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 324
    Processing helix  chain 'A' and resid 369 through 380
      removed outlier: 3.599A  pdb=" N   ASN A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 395
    Processing helix  chain 'A' and resid 404 through 413
    Processing helix  chain 'A' and resid 415 through 430
      removed outlier: 3.555A  pdb=" N   GLU A 420 " --> pdb=" O   SER A 416 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   HIS A 423 " --> pdb=" O   GLU A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 439
      Proline residue:  A 436  - end of helix
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 3.551A  pdb=" N   ASP A 443 " --> pdb=" O   TRP A 439 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ASN A 444 " --> pdb=" O   TYR A 440 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 439 through 444'
    Processing helix  chain 'A' and resid 445 through 454
      removed outlier: 3.637A  pdb=" N   ASN A 449 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ILE A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG A 452 " --> pdb=" O   MET A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 518
    Processing helix  chain 'A' and resid 531 through 542
      removed outlier: 3.916A  pdb=" N   THR A 535 " --> pdb=" O   GLU A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 578
      removed outlier: 3.787A  pdb=" N   VAL A 578 " --> pdb=" O   ILE A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 624
    Processing helix  chain 'A' and resid 647 through 650
    Processing helix  chain 'A' and resid 654 through 680
      removed outlier: 4.894A  pdb=" N   TYR A 665 " --> pdb=" O   LEU A 661 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   SER A 666 " --> pdb=" O   ALA A 662 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS A 678 " --> pdb=" O   ILE A 674 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A 680 " --> pdb=" O   LEU A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 690
      removed outlier: 3.759A  pdb=" N   THR A 685 " --> pdb=" O   ARG A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 722
      removed outlier: 3.903A  pdb=" N   ILE A 707 " --> pdb=" O   ASP A 703 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   MET A 708 " --> pdb=" O   SER A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 752
    Processing helix  chain 'A' and resid 757 through 772
      removed outlier: 3.762A  pdb=" N   GLY A 766 " --> pdb=" O   ALA A 762 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   VAL A 767 " --> pdb=" O   ALA A 763 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   PHE A 770 " --> pdb=" O   GLY A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 781
      removed outlier: 3.779A  pdb=" N   ILE A 777 " --> pdb=" O   TYR A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 796
      removed outlier: 3.868A  pdb=" N   LEU A 796 " --> pdb=" O   ALA A 793 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 793 through 796'
    Processing helix  chain 'A' and resid 797 through 814
    Processing helix  chain 'A' and resid 820 through 824
      removed outlier: 3.798A  pdb=" N   ILE A 824 " --> pdb=" O   TRP A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 832
      removed outlier: 3.827A  pdb=" N   GLY A 831 " --> pdb=" O   SER A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 861
      removed outlier: 3.571A  pdb=" N   VAL A 860 " --> pdb=" O   TYR A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 977
    Processing helix  chain 'A' and resid 988 through 992
    Processing helix  chain 'A' and resid 993 through 997
      removed outlier: 3.842A  pdb=" N   THR A 996 " --> pdb=" O   ASP A 993 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER A 997 " --> pdb=" O   ILE A 994 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 993 through 997'
    Processing helix  chain 'A' and resid 1001 through 1005
      removed outlier: 3.750A  pdb=" N   LEU A1005 " --> pdb=" O   ARG A1002 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1030
      removed outlier: 4.032A  pdb=" N   MET A1024 " --> pdb=" O   VAL A1020 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   LEU A1025 " --> pdb=" O   ALA A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1035 through 1050
      removed outlier: 3.600A  pdb=" N   LEU A1040 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1063 through 1074
      removed outlier: 3.995A  pdb=" N   ARG A1068 " --> pdb=" O   GLY A1064 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS A1069 " --> pdb=" O   GLY A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1093 through 1106
    Processing helix  chain 'A' and resid 1119 through 1127
      removed outlier: 3.609A  pdb=" N   ASP A1124 " --> pdb=" O   MET A1120 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LEU A1125 " --> pdb=" O   ASP A1121 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A1127 " --> pdb=" O   ALA A1123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1149
      removed outlier: 4.436A  pdb=" N   ASN A1149 " --> pdb=" O   LEU A1145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1205 through 1216
      removed outlier: 3.556A  pdb=" N   VAL A1211 " --> pdb=" O   GLU A1207 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL A1212 " --> pdb=" O   LEU A1208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1244 through 1253
    Processing helix  chain 'A' and resid 1268 through 1277
      removed outlier: 3.613A  pdb=" N   ILE A1272 " --> pdb=" O   PRO A1268 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   THR A1277 " --> pdb=" O   PHE A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1350 through 1368
      removed outlier: 3.556A  pdb=" N   GLN A1356 " --> pdb=" O   LEU A1352 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A1357 " --> pdb=" O   GLN A1353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1373 through 1378
    Processing helix  chain 'A' and resid 1378 through 1393
    Processing helix  chain 'A' and resid 1406 through 1410
      removed outlier: 3.890A  pdb=" N   TYR A1410 " --> pdb=" O   PRO A1407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1424 through 1436
    Processing helix  chain 'A' and resid 1470 through 1475
      removed outlier: 3.876A  pdb=" N   GLN A1475 " --> pdb=" O   THR A1471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1530 through 1546
      removed outlier: 3.968A  pdb=" N   LYS A1536 " --> pdb=" O   ASP A1532 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR A1538 " --> pdb=" O   LEU A1534 " (cutoff:3.500A)
      Proline residue:  A1539  - end of helix
    Processing helix  chain 'A' and resid 1575 through 1586
      removed outlier: 3.512A  pdb=" N   PHE A1579 " --> pdb=" O   ALA A1575 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ILE A1586 " --> pdb=" O   ASP A1582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1592 through 1601
      removed outlier: 4.529A  pdb=" N   GLU A1601 " --> pdb=" O   GLU A1597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1601 through 1610
      removed outlier: 3.846A  pdb=" N   PHE A1605 " --> pdb=" O   GLU A1601 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   GLU A1610 " --> pdb=" O   LEU A1606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1626 through 1643
      removed outlier: 3.712A  pdb=" N   LEU A1643 " --> pdb=" O   LEU A1639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1648 through 1652
    Processing helix  chain 'A' and resid 1664 through 1691
      removed outlier: 3.839A  pdb=" N   GLU A1670 " --> pdb=" O   GLU A1666 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE A1671 " --> pdb=" O   GLN A1667 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A1678 " --> pdb=" O   LEU A1674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1691 through 1707
      removed outlier: 3.563A  pdb=" N   ALA A1695 " --> pdb=" O   SER A1691 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASN A1707 " --> pdb=" O   GLN A1703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1709 through 1716
    Processing helix  chain 'A' and resid 1719 through 1747
      removed outlier: 3.682A  pdb=" N   TYR A1723 " --> pdb=" O   SER A1719 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   VAL A1737 " --> pdb=" O   MET A1733 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   SER A1738 " --> pdb=" O   ASN A1734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1750 through 1754
    Processing helix  chain 'A' and resid 1759 through 1779
      removed outlier: 3.909A  pdb=" N   GLY A1771 " --> pdb=" O   LEU A1767 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TRP A1772 " --> pdb=" O   LEU A1768 " (cutoff:3.500A)
      Proline residue:  A1776  - end of helix
    Processing helix  chain 'A' and resid 1780 through 1785
      removed outlier: 3.791A  pdb=" N   LEU A1784 " --> pdb=" O   PRO A1780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1789 through 1813
      removed outlier: 4.117A  pdb=" N   VAL A1793 " --> pdb=" O   SER A1789 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A1798 " --> pdb=" O   ALA A1794 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU A1813 " --> pdb=" O   ILE A1809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1820 through 1831
      removed outlier: 4.195A  pdb=" N   ARG A1824 " --> pdb=" O   ARG A1820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1832 through 1835
      removed outlier: 4.096A  pdb=" N   VAL A1835 " --> pdb=" O   LEU A1832 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1832 through 1835'
    Processing helix  chain 'A' and resid 1836 through 1861
      removed outlier: 3.897A  pdb=" N   ARG A1860 " --> pdb=" O   ASP A1856 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A1861 " --> pdb=" O   VAL A1857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1875 through 1898
      removed outlier: 3.565A  pdb=" N   VAL A1887 " --> pdb=" O   VAL A1883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1978 through 1986
      removed outlier: 3.692A  pdb=" N   MET A1984 " --> pdb=" O   THR A1980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2009 through 2014
    Processing helix  chain 'A' and resid 2033 through 2039
    Processing helix  chain 'A' and resid 2049 through 2056
      removed outlier: 3.627A  pdb=" N   ILE A2055 " --> pdb=" O   ALA A2051 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS A2056 " --> pdb=" O   ASN A2052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2067 through 2071
      removed outlier: 3.796A  pdb=" N   TYR A2071 " --> pdb=" O   ALA A2068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2072 through 2084
      removed outlier: 3.627A  pdb=" N   LYS A2076 " --> pdb=" O   SER A2072 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ARG A2077 " --> pdb=" O   GLY A2073 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2102 through 2120
      removed outlier: 3.802A  pdb=" N   MET A2108 " --> pdb=" O   GLN A2104 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A2119 " --> pdb=" O   SER A2115 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLY A2120 " --> pdb=" O   ILE A2116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2129 through 2136
      removed outlier: 3.513A  pdb=" N   CYS A2133 " --> pdb=" O   SER A2129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2153 through 2161
      removed outlier: 3.543A  pdb=" N   PHE A2161 " --> pdb=" O   LEU A2157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2182 through 2192
    Processing helix  chain 'A' and resid 2215 through 2219
    Processing helix  chain 'A' and resid 2240 through 2249
      removed outlier: 3.623A  pdb=" N   VAL A2244 " --> pdb=" O   THR A2240 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60
      removed outlier: 4.036A  pdb=" N   ILE A1615 " --> pdb=" O   GLY A 631 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   VAL A1617 " --> pdb=" O   TYR A 633 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A1619 " --> pdb=" O   GLN A 635 " (cutoff:3.500A)
      removed outlier: 8.900A  pdb=" N   ILE A1560 " --> pdb=" O   TYR A1414 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   PHE A1416 " --> pdb=" O   ILE A1560 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   ILE A1562 " --> pdb=" O   PHE A1416 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   SER A1418 " --> pdb=" O   ILE A1562 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 527
      removed outlier: 6.235A  pdb=" N   ILE A 398 " --> pdb=" O   GLU A 526 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   LEU A 399 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 566 through 571
    Processing sheet with id=AA5, first strand: chain 'A' and resid 932 through 933
    Processing sheet with id=AA6, first strand: chain 'A' and resid 961 through 962
      removed outlier: 6.414A  pdb=" N   ALA A1131 " --> pdb=" O   LEU A 962 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1007 through 1008
      removed outlier: 6.996A  pdb=" N   CYS A1008 " --> pdb=" O   ASP A1086 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1155 through 1158
      removed outlier: 7.161A  pdb=" N   ILE A1230 " --> pdb=" O   VAL A1222 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2091 through 2094
      removed outlier: 6.588A  pdb=" N   VAL A2092 " --> pdb=" O   VAL A2124 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ILE A2142 " --> pdb=" O   ARG A2149 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2205 through 2209

    624 hydrogen bonds defined for protein.
    1802 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: 5.80

  Time building geometry restraints manager: 6.20 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: 4424
        1.34 -     1.47: 3330
        1.47 -     1.59: 5977
        1.59 -     1.71: 0
        1.71 -     1.83: 76
  Bond restraints: 13807
  Sorted by residual:
  bond pdb=" C1  NAG A2301 "
       pdb=" O5  NAG A2301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 5.96e+00
  bond pdb=" C1  NAG A2303 "
       pdb=" O5  NAG A2303 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.75e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.03e+00
  bond pdb=" C1  MAN C   4 "
       pdb=" C2  MAN C   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.558 -0.032 2.00e-02 2.50e+03 2.52e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.46e+00
  ... (remaining 13802 not shown)

  Histogram of bond angle deviations from ideal:
       99.96 -   106.79: 474
      106.79 -   113.61: 7719
      113.61 -   120.43: 5050
      120.43 -   127.25: 5532
      127.25 -   134.07: 171
  Bond angle restraints: 18946
  Sorted by residual:
  angle pdb=" N   PRO A 458 "
        pdb=" CA  PRO A 458 "
        pdb=" CB  PRO A 458 "
      ideal   model   delta    sigma   weight residual
     103.33  110.51   -7.18 9.30e-01 1.16e+00 5.95e+01
  angle pdb=" N   PRO A 188 "
        pdb=" CA  PRO A 188 "
        pdb=" CB  PRO A 188 "
      ideal   model   delta    sigma   weight residual
     103.00  110.42   -7.42 1.10e+00 8.26e-01 4.55e+01
  angle pdb=" C   CYS A 930 "
        pdb=" CA  CYS A 930 "
        pdb=" CB  CYS A 930 "
      ideal   model   delta    sigma   weight residual
     115.89  110.34    5.55 1.32e+00 5.74e-01 1.77e+01
  angle pdb=" CA  LYS A2049 "
        pdb=" CB  LYS A2049 "
        pdb=" CG  LYS A2049 "
      ideal   model   delta    sigma   weight residual
     114.10  120.65   -6.55 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" C   ASN A1442 "
        pdb=" CA  ASN A1442 "
        pdb=" CB  ASN A1442 "
      ideal   model   delta    sigma   weight residual
     109.80  115.02   -5.22 1.61e+00 3.86e-01 1.05e+01
  ... (remaining 18941 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 7396
       17.77 -    35.55: 495
       35.55 -    53.32: 91
       53.32 -    71.10: 16
       71.10 -    88.87: 9
  Dihedral angle restraints: 8007
    sinusoidal: 2391
      harmonic: 5616
  Sorted by residual:
  dihedral pdb=" CB  CYS A1488 "
           pdb=" SG  CYS A1488 "
           pdb=" SG  CYS A1502 "
           pdb=" CB  CYS A1502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    7.50   85.50     1      1.00e+01 1.00e-02 8.85e+01
  dihedral pdb=" CB  CYS A 641 "
           pdb=" SG  CYS A 641 "
           pdb=" SG  CYS A1490 "
           pdb=" CB  CYS A1490 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.90  -68.90     1      1.00e+01 1.00e-02 6.14e+01
  dihedral pdb=" CA  MET A1587 "
           pdb=" C   MET A1587 "
           pdb=" N   ASN A1588 "
           pdb=" CA  ASN A1588 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.07   26.93     0      5.00e+00 4.00e-02 2.90e+01
  ... (remaining 8004 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1911
       0.055 -    0.111: 366
       0.111 -    0.166: 30
       0.166 -    0.222: 3
       0.222 -    0.277: 3
  Chirality restraints: 2313
  Sorted by residual:
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CA  PRO A 188 "
            pdb=" N   PRO A 188 "
            pdb=" C   PRO A 188 "
            pdb=" CB  PRO A 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 2310 not shown)

  Planarity restraints: 2444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 774 "   -0.052 5.00e-02 4.00e+02   7.73e-02 9.57e+00
        pdb=" N   PRO A 775 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 775 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 775 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 435 "   -0.047 5.00e-02 4.00e+02   7.10e-02 8.06e+00
        pdb=" N   PRO A 436 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 436 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 436 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A1588 "    0.026 2.00e-02 2.50e+03   2.36e-02 6.97e+00
        pdb=" CG  ASN A1588 "   -0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN A1588 "    0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A1588 "   -0.027 2.00e-02 2.50e+03
        pdb=" C1  NAG A2303 "    0.027 2.00e-02 2.50e+03
  ... (remaining 2441 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2268
        2.76 -     3.30: 13644
        3.30 -     3.83: 21952
        3.83 -     4.37: 23402
        4.37 -     4.90: 41608
  Nonbonded interactions: 102874
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 295 "
            pdb=" OG1 THR A 300 "
     model   vdw
     2.226 2.440
  nonbonded pdb=" O   VAL A1160 "
            pdb=" OG  SER A1261 "
     model   vdw
     2.249 2.440
  nonbonded pdb=" O   PHE A  56 "
            pdb=" NE2 GLN A 635 "
     model   vdw
     2.254 2.520
  nonbonded pdb=" OE2 GLU A  89 "
            pdb=" NE2 GLN A 635 "
     model   vdw
     2.255 2.520
  nonbonded pdb=" O   ARG A1241 "
            pdb=" OG  SER A1245 "
     model   vdw
     2.261 2.440
  ... (remaining 102869 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=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          10.400
  Check model and map are aligned:         0.200
  Set scattering table:                    0.120
  Process input model:                     50.250
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.090
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   70.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
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      :  0.003   0.049  13807  Z= 0.201
  Angle     :  0.613   8.948  18946  Z= 0.314
  Chirality :  0.044   0.277   2313
  Planarity :  0.005   0.077   2438
  Dihedral  : 13.096  88.869   4350
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.37 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  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: -0.96 (0.20), residues: 1911
  helix:  1.20 (0.19), residues: 869
  sheet: -0.77 (0.49), residues: 139
  loop : -2.61 (0.20), residues: 903

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.521 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.2133
  time to fit residues: 69.8446
Evaluate side-chains
  175 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.653 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.0128
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 162 optimal weight:    0.9990
   chunk 146 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 98 optimal weight:    9.9990
   chunk 78 optimal weight:    3.9990
   chunk 151 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0030
   chunk 112 optimal weight:    0.0030
   chunk 175 optimal weight:    2.9990
   overall best weight:    0.8004

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 721 HIS
A1442 ASN
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13807  Z= 0.203
  Angle     :  0.592   9.151  18946  Z= 0.296
  Chirality :  0.044   0.272   2313
  Planarity :  0.005   0.066   2438
  Dihedral  :  4.048  25.442   2022
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.69 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  8.28 %
    Favored  : 90.65 %
  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: -1.02 (0.20), residues: 1911
  helix:  1.10 (0.18), residues: 894
  sheet: -0.66 (0.47), residues: 137
  loop : -2.72 (0.20), residues: 880

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 185
  time to evaluate  : 1.521 
Fit side-chains
  outliers start: 12
  outliers final: 7
  residues processed: 191
  average time/residue: 0.2070
  time to fit residues: 62.5133
Evaluate side-chains
  184 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 177
  time to evaluate  : 1.480 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1263
  time to fit residues: 3.5694
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 145 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   chunk 48 optimal weight:    0.2980
   chunk 175 optimal weight:    1.9990
   chunk 189 optimal weight:    0.9990
   chunk 156 optimal weight:    2.9990
   chunk 174 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 140 optimal weight:    0.8980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13807  Z= 0.223
  Angle     :  0.598   9.497  18946  Z= 0.299
  Chirality :  0.044   0.281   2313
  Planarity :  0.005   0.062   2438
  Dihedral  :  4.173  23.651   2022
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 10.21 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.95 %
    Favored  : 88.07 %
  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: -1.15 (0.20), residues: 1911
  helix:  0.98 (0.18), residues: 899
  sheet: -1.01 (0.46), residues: 144
  loop : -2.75 (0.20), residues: 868

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 187
  time to evaluate  : 1.471 
Fit side-chains
  outliers start: 11
  outliers final: 5
  residues processed: 193
  average time/residue: 0.2119
  time to fit residues: 64.8477
Evaluate side-chains
  180 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 175
  time to evaluate  : 1.455 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1195
  time to fit residues: 3.1245
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 173 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 117 optimal weight:   20.0000
   chunk 176 optimal weight:    5.9990
   chunk 186 optimal weight:    9.9990
   chunk 92 optimal weight:    0.4980
   chunk 167 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS
** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13807  Z= 0.250
  Angle     :  0.615   9.578  18946  Z= 0.308
  Chirality :  0.045   0.286   2313
  Planarity :  0.005   0.060   2438
  Dihedral  :  4.344  22.615   2022
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 10.52 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 12.82 %
    Favored  : 86.11 %
  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: -1.25 (0.20), residues: 1911
  helix:  0.88 (0.18), residues: 898
  sheet: -1.21 (0.45), residues: 146
  loop : -2.74 (0.20), residues: 867

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 184
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 4
  residues processed: 186
  average time/residue: 0.2072
  time to fit residues: 61.7718
Evaluate side-chains
  178 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 174
  time to evaluate  : 1.448 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1234
  time to fit residues: 2.8869
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 155 optimal weight:    0.0980
   chunk 105 optimal weight:    0.0070
   chunk 2 optimal weight:    2.9990
   chunk 138 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 159 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 95 optimal weight:    0.5980
   chunk 167 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6800

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS
** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13807  Z= 0.182
  Angle     :  0.581   9.464  18946  Z= 0.289
  Chirality :  0.043   0.278   2313
  Planarity :  0.004   0.058   2438
  Dihedral  :  4.196  20.315   2022
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.00 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 14.69 %
    Favored  : 84.33 %
  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: -1.15 (0.20), residues: 1911
  helix:  1.00 (0.18), residues: 899
  sheet: -0.96 (0.46), residues: 139
  loop : -2.77 (0.20), residues: 873

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 182
  time to evaluate  : 1.522 
Fit side-chains
  outliers start: 11
  outliers final: 5
  residues processed: 185
  average time/residue: 0.2130
  time to fit residues: 63.7016
Evaluate side-chains
  181 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 176
  time to evaluate  : 1.526 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1279
  time to fit residues: 3.2397
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 168 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 109 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 186 optimal weight:   10.0000
   chunk 155 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   chunk 61 optimal weight:    0.7980
   chunk 98 optimal weight:    8.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS
** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13807  Z= 0.248
  Angle     :  0.619   9.609  18946  Z= 0.309
  Chirality :  0.044   0.284   2313
  Planarity :  0.005   0.058   2438
  Dihedral  :  4.343  21.433   2022
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.37 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 15.76 %
    Favored  : 83.62 %
  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: -1.23 (0.20), residues: 1911
  helix:  0.90 (0.18), residues: 898
  sheet: -1.20 (0.46), residues: 146
  loop : -2.74 (0.20), residues: 867

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 175
  time to evaluate  : 1.600 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 180
  average time/residue: 0.2543
  time to fit residues: 75.1517
Evaluate side-chains
  175 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 171
  time to evaluate  : 1.483 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1346
  time to fit residues: 3.0551
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 180 optimal weight:    5.9990
   chunk 21 optimal weight:    0.4980
   chunk 106 optimal weight:    0.0970
   chunk 136 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 157 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0980
   chunk 186 optimal weight:   10.0000
   chunk 116 optimal weight:    0.0040
   chunk 113 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.2990

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS
** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13807  Z= 0.157
  Angle     :  0.568   9.423  18946  Z= 0.282
  Chirality :  0.042   0.273   2313
  Planarity :  0.004   0.058   2438
  Dihedral  :  4.097  18.456   2022
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.58 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 15.94 %
    Favored  : 83.26 %
  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: -1.03 (0.20), residues: 1911
  helix:  1.11 (0.18), residues: 897
  sheet: -0.64 (0.52), residues: 120
  loop : -2.74 (0.20), residues: 894

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 186
  time to evaluate  : 1.467 
Fit side-chains
  outliers start: 9
  outliers final: 2
  residues processed: 190
  average time/residue: 0.2121
  time to fit residues: 65.5125
Evaluate side-chains
  182 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 180
  time to evaluate  : 1.502 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1471
  time to fit residues: 2.7113
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 118 optimal weight:    0.8980
   chunk 126 optimal weight:    0.3980
   chunk 91 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 146 optimal weight:    0.9980
   chunk 169 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS
** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13807  Z= 0.188
  Angle     :  0.586   9.559  18946  Z= 0.290
  Chirality :  0.043   0.275   2313
  Planarity :  0.004   0.058   2438
  Dihedral  :  4.112  19.298   2022
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.74 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 16.12 %
    Favored  : 83.26 %
  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: -1.05 (0.20), residues: 1911
  helix:  1.10 (0.18), residues: 897
  sheet: -0.72 (0.52), residues: 120
  loop : -2.75 (0.20), residues: 894

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 179
  time to evaluate  : 1.471 
Fit side-chains
  outliers start: 7
  outliers final: 1
  residues processed: 181
  average time/residue: 0.2033
  time to fit residues: 59.8125
Evaluate side-chains
  175 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 174
  time to evaluate  : 1.484 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1406
  time to fit residues: 2.3299
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 178 optimal weight:    1.9990
   chunk 162 optimal weight:    9.9990
   chunk 173 optimal weight:    0.0870
   chunk 104 optimal weight:    9.9990
   chunk 75 optimal weight:    4.9990
   chunk 136 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 156 optimal weight:    3.9990
   chunk 163 optimal weight:    9.9990
   chunk 172 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    1.5364

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

Flipped N/Q/H residues before XYZ refinement:
A 617 GLN
A 721 HIS
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13807  Z= 0.288
  Angle     :  0.656   9.652  18946  Z= 0.329
  Chirality :  0.045   0.286   2313
  Planarity :  0.005   0.058   2438
  Dihedral  :  4.531  21.921   2022
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.83 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 16.74 %
    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: -1.31 (0.20), residues: 1911
  helix:  0.86 (0.18), residues: 898
  sheet: -1.34 (0.47), residues: 139
  loop : -2.79 (0.20), residues: 874

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 175
  time to evaluate  : 1.463 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 177
  average time/residue: 0.2112
  time to fit residues: 60.5198
Evaluate side-chains
  172 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 1.473 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1259
  time to fit residues: 2.2719
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 183 optimal weight:    0.9990
   chunk 111 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 127 optimal weight:    0.9980
   chunk 192 optimal weight:    4.9990
   chunk 176 optimal weight:    2.9990
   chunk 153 optimal weight:    0.0370
   chunk 15 optimal weight:    0.4980
   chunk 118 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0470
   chunk 121 optimal weight:   10.0000
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13807  Z= 0.173
  Angle     :  0.592   9.460  18946  Z= 0.295
  Chirality :  0.043   0.269   2313
  Planarity :  0.004   0.057   2438
  Dihedral  :  4.258  20.842   2022
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.37 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 17.10 %
    Favored  : 82.37 %
  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: -1.12 (0.20), residues: 1911
  helix:  1.00 (0.18), residues: 894
  sheet: -0.70 (0.53), residues: 120
  loop : -2.71 (0.20), residues: 897

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 179
  time to evaluate  : 1.368 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 182
  average time/residue: 0.2148
  time to fit residues: 62.4846
Evaluate side-chains
  177 residues out of total 1705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 175
  time to evaluate  : 1.534 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1418
  time to fit residues: 2.4419
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 163 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 141 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 153 optimal weight:    0.0170
   chunk 64 optimal weight:    0.8980
   chunk 157 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 134 optimal weight:    3.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS
A1442 ASN
** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1878 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.161437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.141580 restraints weight = 28801.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.142276 restraints weight = 20771.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.143390 restraints weight = 15655.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4009 r_free = 0.4009    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4008 r_free = 0.4008    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13807  Z= 0.191
  Angle     :  0.603   9.551  18946  Z= 0.299
  Chirality :  0.043   0.272   2313
  Planarity :  0.005   0.079   2438
  Dihedral  :  4.207  19.717   2022
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.47 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 17.19 %
    Favored  : 82.46 %
  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: -1.10 (0.20), residues: 1911
  helix:  1.01 (0.18), residues: 898
  sheet: -0.69 (0.53), residues: 120
  loop : -2.72 (0.20), residues: 893
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2748.81 seconds
wall clock time: 50 minutes 52.47 seconds (3052.47 seconds total)